From 367f3c8d21ed0af944427072402d9b4ac6453b02 Mon Sep 17 00:00:00 2001 From: emerbitz <78315455+emerbitz@users.noreply.github.com> Date: Fri, 19 Dec 2025 21:04:21 +0100 Subject: [PATCH 1/4] add bond order for CX atom type --- src/gmxtop/constants.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/gmxtop/constants.py b/src/gmxtop/constants.py index 704b5b4..2cb18da 100644 --- a/src/gmxtop/constants.py +++ b/src/gmxtop/constants.py @@ -197,6 +197,7 @@ "N3": 4, "P": 4, "SO": 4, + "CX": 4, } AA3 = [ From 49753cc0b4820f51d8e11f3ad4f04d8be8c51954 Mon Sep 17 00:00:00 2001 From: emerbitz <78315455+emerbitz@users.noreply.github.com> Date: Fri, 19 Dec 2025 21:05:10 +0100 Subject: [PATCH 2/4] add test for baz --- tests/test_topology.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/tests/test_topology.py b/tests/test_topology.py index 17d9cf6..67ec1d8 100644 --- a/tests/test_topology.py +++ b/tests/test_topology.py @@ -622,3 +622,12 @@ def test_get_improper_dihedrals_dimer(self, top_target: Topology): "46", top_target.ff ) assert list(atom_impropers.keys()) == [("46", "53", "51", "52")] + + +class TestBAZ: + def test_no_warning_on_loading(self, filedir, caplog): + caplog.set_level(logging.WARNING) + Topology.from_path(filedir / "baz.top", ffdir=filedir / "amber14sb.ff") + assert ( + not caplog.records + ), f"Logger.warning was raised during loading baz.top: {[r.message for r in caplog.records]}" From 39f6c23233d3cba1fefc727e033f411072f39685 Mon Sep 17 00:00:00 2001 From: emerbitz <78315455+emerbitz@users.noreply.github.com> Date: Fri, 19 Dec 2025 21:07:16 +0100 Subject: [PATCH 3/4] add baz.top and amber14sbff as testfiles --- .../assets/amber14sb.ff/Makefile.am | 20 + .../assets/amber14sb.ff/Makefile.in | 444 +++ .../assets/amber14sb.ff/aminoacids.arn | 83 + .../assets/amber14sb.ff/aminoacids.c.tdb | 3 + .../assets/amber14sb.ff/aminoacids.hdb | 518 +++ .../assets/amber14sb.ff/aminoacids.n.tdb | 3 + .../assets/amber14sb.ff/aminoacids.r2b | 31 + .../assets/amber14sb.ff/aminoacids.rtp | 3401 +++++++++++++++++ .../assets/amber14sb.ff/aminoacids.vsd | 225 ++ .../assets/amber14sb.ff/atomtypes.atp | 84 + tests/test_files/assets/amber14sb.ff/dna.arn | 8 + tests/test_files/assets/amber14sb.ff/dna.hdb | 160 + tests/test_files/assets/amber14sb.ff/dna.r2b | 6 + tests/test_files/assets/amber14sb.ff/dna.rtp | 1223 ++++++ .../assets/amber14sb.ff/ffbonded.itp | 1401 +++++++ .../assets/amber14sb.ff/ffnonbonded.itp | 93 + .../assets/amber14sb.ff/forcefield.doc | 12 + .../assets/amber14sb.ff/forcefield.itp | 23 + tests/test_files/assets/amber14sb.ff/gbsa.itp | 38 + tests/test_files/assets/amber14sb.ff/ions.itp | 88 + tests/test_files/assets/amber14sb.ff/rna.arn | 8 + tests/test_files/assets/amber14sb.ff/rna.hdb | 205 + tests/test_files/assets/amber14sb.ff/rna.r2b | 6 + tests/test_files/assets/amber14sb.ff/rna.rtp | 1232 ++++++ tests/test_files/assets/amber14sb.ff/spc.itp | 33 + tests/test_files/assets/amber14sb.ff/spce.itp | 33 + .../test_files/assets/amber14sb.ff/tip3p.itp | 34 + .../test_files/assets/amber14sb.ff/tip4p.itp | 55 + .../assets/amber14sb.ff/tip4pew.itp | 56 + .../test_files/assets/amber14sb.ff/tip5p.itp | 69 + tests/test_files/assets/amber14sb.ff/urea.itp | 36 + .../assets/amber14sb.ff/watermodels.dat | 5 + tests/test_files/test_topology/amber14sb.ff | 1 + tests/test_files/test_topology/baz.top | 237 ++ 34 files changed, 9874 insertions(+) create mode 100644 tests/test_files/assets/amber14sb.ff/Makefile.am create mode 100644 tests/test_files/assets/amber14sb.ff/Makefile.in create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.arn create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.c.tdb create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.hdb create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.n.tdb create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.r2b create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.rtp create mode 100644 tests/test_files/assets/amber14sb.ff/aminoacids.vsd create mode 100644 tests/test_files/assets/amber14sb.ff/atomtypes.atp create mode 100644 tests/test_files/assets/amber14sb.ff/dna.arn create mode 100644 tests/test_files/assets/amber14sb.ff/dna.hdb create mode 100644 tests/test_files/assets/amber14sb.ff/dna.r2b create mode 100644 tests/test_files/assets/amber14sb.ff/dna.rtp create mode 100644 tests/test_files/assets/amber14sb.ff/ffbonded.itp create mode 100644 tests/test_files/assets/amber14sb.ff/ffnonbonded.itp create mode 100644 tests/test_files/assets/amber14sb.ff/forcefield.doc create mode 100644 tests/test_files/assets/amber14sb.ff/forcefield.itp create mode 100644 tests/test_files/assets/amber14sb.ff/gbsa.itp create mode 100644 tests/test_files/assets/amber14sb.ff/ions.itp create mode 100644 tests/test_files/assets/amber14sb.ff/rna.arn create mode 100644 tests/test_files/assets/amber14sb.ff/rna.hdb create mode 100644 tests/test_files/assets/amber14sb.ff/rna.r2b create mode 100644 tests/test_files/assets/amber14sb.ff/rna.rtp create mode 100644 tests/test_files/assets/amber14sb.ff/spc.itp create mode 100644 tests/test_files/assets/amber14sb.ff/spce.itp create mode 100644 tests/test_files/assets/amber14sb.ff/tip3p.itp create mode 100644 tests/test_files/assets/amber14sb.ff/tip4p.itp create mode 100644 tests/test_files/assets/amber14sb.ff/tip4pew.itp create mode 100644 tests/test_files/assets/amber14sb.ff/tip5p.itp create mode 100644 tests/test_files/assets/amber14sb.ff/urea.itp create mode 100644 tests/test_files/assets/amber14sb.ff/watermodels.dat create mode 120000 tests/test_files/test_topology/amber14sb.ff create mode 100644 tests/test_files/test_topology/baz.top diff --git a/tests/test_files/assets/amber14sb.ff/Makefile.am b/tests/test_files/assets/amber14sb.ff/Makefile.am new file mode 100644 index 0000000..f2c53bd --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/Makefile.am @@ -0,0 +1,20 @@ +## Process this file with automake to produce Makefile.in +# +# Don't edit - this file is generated automatically from Makefile.am +# +topoldir = ${pkgdatadir}/top/amber14sb.ff + +topol_DATA = \ + aminoacids.arn aminoacids.vsd \ + aminoacids.c.tdb atomtypes.atp ffnonbonded.itp \ + aminoacids.hdb forcefield.doc dna.rtp dna.r2b dna.arn dna.hdb \ + aminoacids.n.tdb forcefield.itp rna.rtp rna.r2b rna.arn rna.hdb \ + aminoacids.r2b ffbonded.itp tip3p.itp urea.itp \ + aminoacids.rtp ions.itp tip4p.itp \ + tip4pew.itp tip5p.itp watermodels.dat gbsa.itp \ + spc.itp spce.itp + +EXTRA_DIST = ${topol_DATA} + +CLEANFILES = *~ \\\#* + diff --git a/tests/test_files/assets/amber14sb.ff/Makefile.in b/tests/test_files/assets/amber14sb.ff/Makefile.in new file mode 100644 index 0000000..3b4960f --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/Makefile.in @@ -0,0 +1,444 @@ +# Makefile.in generated by automake 1.11 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, +# Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + +VPATH = @srcdir@ +pkgdatadir = $(datadir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = @build@ +host_triplet = @host@ +subdir = share/top/amber14sb.ff +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \ + $(top_srcdir)/configure.ac +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(SHELL) $(top_srcdir)/config/mkinstalldirs +CONFIG_HEADER = $(top_builddir)/src/config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +SOURCES = +DIST_SOURCES = +am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; +am__vpath_adj = case $$p in \ + $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \ + *) f=$$p;; \ + esac; +am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`; +am__install_max = 40 +am__nobase_strip_setup = \ + srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'` +am__nobase_strip = \ + for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||" +am__nobase_list = $(am__nobase_strip_setup); \ + for p in $$list; do echo "$$p $$p"; done | \ + sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \ + $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \ + if (++n[$$2] == $(am__install_max)) \ + { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \ + END { for (dir in files) print dir, files[dir] }' +am__base_list = \ + sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \ + sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g' +am__installdirs = "$(DESTDIR)$(topoldir)" +DATA = $(topol_DATA) +DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +ACLOCAL = @ACLOCAL@ +AMTAR = @AMTAR@ +AR = @AR@ +AS = @AS@ +ASFLAGS = @ASFLAGS@ +AUTOCONF = @AUTOCONF@ +AUTOHEADER = @AUTOHEADER@ +AUTOMAKE = @AUTOMAKE@ +AWK = @AWK@ +CC = @CC@ +CCAS = @CCAS@ +CCASDEPMODE = @CCASDEPMODE@ +CCASFLAGS = @CCASFLAGS@ +CCDEPMODE = @CCDEPMODE@ +CC_FOR_BUILD = @CC_FOR_BUILD@ +CFLAGS = @CFLAGS@ +CPP = @CPP@ +CPPFLAGS = @CPPFLAGS@ +CXX = @CXX@ +CXXCPP = @CXXCPP@ +CXXDEPMODE = @CXXDEPMODE@ +CXXFLAGS = @CXXFLAGS@ +CYGPATH_W = @CYGPATH_W@ +DEFS = @DEFS@ +DEPDIR = @DEPDIR@ +DLLTOOL = @DLLTOOL@ +DLOPEN_LIBS = @DLOPEN_LIBS@ +ECHO = @ECHO@ +ECHO_C = @ECHO_C@ +ECHO_N = @ECHO_N@ +ECHO_T = @ECHO_T@ +EGREP = @EGREP@ +EXEEXT = @EXEEXT@ +F77 = @F77@ +F77LINK = @F77LINK@ +FFLAGS = @FFLAGS@ +FFT_LIBS = @FFT_LIBS@ +FLIBS = @FLIBS@ +GREP = @GREP@ +GSL_LIBS = @GSL_LIBS@ +INCLUDES = @INCLUDES@ +INSTALL = @INSTALL@ +INSTALL_DATA = @INSTALL_DATA@ +INSTALL_PROGRAM = @INSTALL_PROGRAM@ +INSTALL_SCRIPT = @INSTALL_SCRIPT@ +INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ +LDFLAGS = @LDFLAGS@ +LIBOBJS = @LIBOBJS@ +LIBS = @LIBS@ +LIBSUFFIX = @LIBSUFFIX@ +LIBTOOL = @LIBTOOL@ +LMKL = @LMKL@ +LN_S = @LN_S@ +LTLIBOBJS = @LTLIBOBJS@ +MAKEINFO = @MAKEINFO@ +MKDIR_P = @MKDIR_P@ +MPICC = @MPICC@ +OBJDUMP = @OBJDUMP@ +OBJEXT = @OBJEXT@ +PACKAGE = @PACKAGE@ +PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ +PACKAGE_NAME = @PACKAGE_NAME@ +PACKAGE_STRING = @PACKAGE_STRING@ +PACKAGE_TARNAME = @PACKAGE_TARNAME@ +PACKAGE_URL = @PACKAGE_URL@ +PACKAGE_VERSION = @PACKAGE_VERSION@ +PATH_SEPARATOR = @PATH_SEPARATOR@ +PKG_CFLAGS = @PKG_CFLAGS@ +PKG_FFT = @PKG_FFT@ +PKG_FFT_LIBS = @PKG_FFT_LIBS@ +PKG_GSL = @PKG_GSL@ +PKG_XML = @PKG_XML@ +PTHREAD_CC = @PTHREAD_CC@ +PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ +PTHREAD_LIBS = @PTHREAD_LIBS@ +RANLIB = @RANLIB@ +RPM = @RPM@ +SET_MAKE = @SET_MAKE@ +SHARED_VERSION_INFO = @SHARED_VERSION_INFO@ +SHELL = @SHELL@ +STRIP = @STRIP@ +VERSION = @VERSION@ +XMKMF = @XMKMF@ +XML_LIBS = @XML_LIBS@ +X_CFLAGS = @X_CFLAGS@ +X_EXTRA_LIBS = @X_EXTRA_LIBS@ +X_LIBS = @X_LIBS@ +X_PRE_LIBS = @X_PRE_LIBS@ +abs_builddir = @abs_builddir@ +abs_srcdir = @abs_srcdir@ +abs_top_builddir = @abs_top_builddir@ +abs_top_srcdir = @abs_top_srcdir@ +ac_ct_CC = @ac_ct_CC@ +ac_ct_CXX = @ac_ct_CXX@ +ac_ct_F77 = @ac_ct_F77@ +am__include = @am__include@ +am__leading_dot = @am__leading_dot@ +am__quote = @am__quote@ +am__tar = @am__tar@ +am__untar = @am__untar@ +bindir = @bindir@ +build = @build@ +build_alias = @build_alias@ +build_cpu = @build_cpu@ +build_os = @build_os@ +build_vendor = @build_vendor@ +builddir = @builddir@ +datadir = @datadir@ +datarootdir = @datarootdir@ +docdir = @docdir@ +dvidir = @dvidir@ +exec_prefix = @exec_prefix@ +have_git = @have_git@ +host = @host@ +host_alias = @host_alias@ +host_cpu = @host_cpu@ +host_os = @host_os@ +host_vendor = @host_vendor@ +htmldir = @htmldir@ +includedir = @includedir@ +infodir = @infodir@ +install_sh = @install_sh@ +libdir = @libdir@ +libexecdir = @libexecdir@ +localedir = @localedir@ +localstatedir = @localstatedir@ +mandir = @mandir@ +mkdir_p = @mkdir_p@ +oldincludedir = @oldincludedir@ +pdfdir = @pdfdir@ +prefix = @prefix@ +program_transform_name = @program_transform_name@ +psdir = @psdir@ +sbindir = @sbindir@ +sharedstatedir = @sharedstatedir@ +srcdir = @srcdir@ +sysconfdir = @sysconfdir@ +target_alias = @target_alias@ +top_build_prefix = @top_build_prefix@ +top_builddir = @top_builddir@ +top_srcdir = @top_srcdir@ + +# +# Don't edit - this file is generated automatically from Makefile.am +# +topoldir = ${pkgdatadir}/top/amber14sb.ff +topol_DATA = \ + aminoacids.arn aminoacids.vsd \ + aminoacids.c.tdb atomtypes.atp ffnonbonded.itp \ + aminoacids.hdb forcefield.doc dna.rtp dna.r2b dna.arn dna.hdb \ + aminoacids.n.tdb forcefield.itp rna.rtp rna.r2b rna.arn rna.hdb \ + aminoacids.r2b ffbonded.itp tip3p.itp urea.itp \ + aminoacids.rtp ions.itp tip4p.itp \ + tip4pew.itp tip5p.itp watermodels.dat gbsa.itp \ + spc.itp spce.itp + +EXTRA_DIST = ${topol_DATA} +CLEANFILES = *~ \\\#* +all: all-am + +.SUFFIXES: +$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) + @for dep in $?; do \ + case '$(am__configure_deps)' in \ + *$$dep*) \ + ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \ + && { if test -f $@; then exit 0; else break; fi; }; \ + exit 1;; \ + esac; \ + done; \ + echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu share/top/amber14sb.ff/Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --gnu share/top/amber14sb.ff/Makefile +.PRECIOUS: Makefile +Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status + @case '$?' in \ + *config.status*) \ + cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ + *) \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \ + esac; + +$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) + cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh + +$(top_srcdir)/configure: $(am__configure_deps) + cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh +$(ACLOCAL_M4): $(am__aclocal_m4_deps) + cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh +$(am__aclocal_m4_deps): + +mostlyclean-libtool: + -rm -f *.lo + +clean-libtool: + -rm -rf .libs _libs +install-topolDATA: $(topol_DATA) + @$(NORMAL_INSTALL) + test -z "$(topoldir)" || $(MKDIR_P) "$(DESTDIR)$(topoldir)" + @list='$(topol_DATA)'; test -n "$(topoldir)" || list=; \ + for p in $$list; do \ + if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ + echo "$$d$$p"; \ + done | $(am__base_list) | \ + while read files; do \ + echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(topoldir)'"; \ + $(INSTALL_DATA) $$files "$(DESTDIR)$(topoldir)" || exit $$?; \ + done + +uninstall-topolDATA: + @$(NORMAL_UNINSTALL) + @list='$(topol_DATA)'; test -n "$(topoldir)" || list=; \ + files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \ + test -n "$$files" || exit 0; \ + echo " ( cd '$(DESTDIR)$(topoldir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(topoldir)" && rm -f $$files +tags: TAGS +TAGS: + +ctags: CTAGS +CTAGS: + + +distdir: $(DISTFILES) + @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ + topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ + list='$(DISTFILES)'; \ + dist_files=`for file in $$list; do echo $$file; done | \ + sed -e "s|^$$srcdirstrip/||;t" \ + -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \ + case $$dist_files in \ + */*) $(MKDIR_P) `echo "$$dist_files" | \ + sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \ + sort -u` ;; \ + esac; \ + for file in $$dist_files; do \ + if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ + if test -d $$d/$$file; then \ + dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ + if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ + else \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ + || exit 1; \ + fi; \ + done +check-am: all-am +check: check-am +all-am: Makefile $(DATA) +installdirs: + for dir in "$(DESTDIR)$(topoldir)"; do \ + test -z "$$dir" || $(MKDIR_P) "$$dir"; \ + done +install: install-am +install-exec: install-exec-am +install-data: install-data-am +uninstall: uninstall-am + +install-am: all-am + @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am + +installcheck: installcheck-am +install-strip: + $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \ + install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \ + `test -z '$(STRIP)' || \ + echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install +mostlyclean-generic: + +clean-generic: + -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES) + +distclean-generic: + -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) + +maintainer-clean-generic: + @echo "This command is intended for maintainers to use" + @echo "it deletes files that may require special tools to rebuild." +clean: clean-am + +clean-am: clean-generic clean-libtool mostlyclean-am + +distclean: distclean-am + -rm -f Makefile +distclean-am: clean-am distclean-generic + +dvi: dvi-am + +dvi-am: + +html: html-am + +html-am: + +info: info-am + +info-am: + +install-data-am: install-topolDATA + +install-dvi: install-dvi-am + +install-dvi-am: + +install-exec-am: + +install-html: install-html-am + +install-html-am: + +install-info: install-info-am + +install-info-am: + +install-man: + +install-pdf: install-pdf-am + +install-pdf-am: + +install-ps: install-ps-am + +install-ps-am: + +installcheck-am: + +maintainer-clean: maintainer-clean-am + -rm -f Makefile +maintainer-clean-am: distclean-am maintainer-clean-generic + +mostlyclean: mostlyclean-am + +mostlyclean-am: mostlyclean-generic mostlyclean-libtool + +pdf: pdf-am + +pdf-am: + +ps: ps-am + +ps-am: + +uninstall-am: uninstall-topolDATA + +.MAKE: install-am install-strip + +.PHONY: all all-am check check-am clean clean-generic clean-libtool \ + distclean distclean-generic distclean-libtool distdir dvi \ + dvi-am html html-am info info-am install install-am \ + install-data install-data-am install-dvi install-dvi-am \ + install-exec install-exec-am install-html install-html-am \ + install-info install-info-am install-man install-pdf \ + install-pdf-am install-ps install-ps-am install-strip \ + install-topolDATA installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \ + uninstall uninstall-am uninstall-topolDATA + + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.arn b/tests/test_files/assets/amber14sb.ff/aminoacids.arn new file mode 100644 index 0000000..5da55ea --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.arn @@ -0,0 +1,83 @@ +; atom renaming specification +; residue gromacs forcefield + NALA H H1 + NGLY H H1 + NSER H H1 + NTHR H H1 + NLEU H H1 + NILE H H1 + NVAL H H1 + NASN H H1 + NGLN H H1 + NARG H H1 + NHID H H1 + NHIE H H1 + NHIP H H1 + NTRP H H1 + NPHE H H1 + NTYR H H1 + NGLU H H1 + NASP H H1 + NLYS H H1 + NPRO H H1 + NCYS H H1 + NCYX H H1 + NMET H H1 + NGLH H H1 + NASP H H1 +; This mapping of O->OC2 and OXT->OC1 might look a bit strange, +; but when we rebuild an oxygen it will be placed directly after C, so +; this mapping makes sure OC1 comes before OC2. The oxygens are anyway chemically +; equivalent, and if you already had their coordinates present they will be kept intact. + CALA O OC2 + CALA OXT OC1 + CGLY O OC2 + CGLY OXT OC1 + CSER O OC2 + CSER OXT OC1 + CTHR O OC2 + CTHR OXT OC1 + CLEU O OC2 + CLEU OXT OC1 + CILE O OC2 + CILE OXT OC1 + CVAL O OC2 + CVAL OXT OC1 + CASN O OC2 + CASN OXT OC1 + CGLN O OC2 + CGLN OXT OC1 + CARG O OC2 + CARG OXT OC1 + CHID O OC2 + CHID OXT OC1 + CHIE O OC2 + CHIE OXT OC1 + CHIP O OC2 + CHIP OXT OC1 + CTRP O OC2 + CTRP OXT OC1 + CPHE O OC2 + CPHE OXT OC1 + CTYR O OC2 + CTYR OXT OC1 + CGLU O OC2 + CGLU OXT OC1 + CASP O OC2 + CASP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 + CPRO O OC2 + CPRO OXT OC1 + CCYS O OC2 + CCYS OXT OC1 + CCYX O OC2 + CCYX OXT OC1 + CMET O OC2 + CMET OXT OC1 + CGLH O OC2 + CGLH OXT OC1 + CASH O OC2 + CASH OXT OC1 + + diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.c.tdb b/tests/test_files/assets/amber14sb.ff/aminoacids.c.tdb new file mode 100644 index 0000000..50d0742 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.c.tdb @@ -0,0 +1,3 @@ +; empty + + diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.hdb b/tests/test_files/assets/amber14sb.ff/aminoacids.hdb new file mode 100644 index 0000000..4df9813 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.hdb @@ -0,0 +1,518 @@ +HOH 1 +2 7 HW OW +HO4 1 +3 10 HW OW +ACE 1 +3 4 HH3 CH3 C O +NME 2 +1 1 H N -C CH3 +3 4 HH3 CH3 N -C +NHE 1 +2 3 H N -C -CA +NH2 1 +2 3 H N -C -CA +ALA 3 +1 1 H N -C CA +1 5 HA CA N CB C +3 4 HB CB CA N +GLY 2 +1 1 H N -C CA +2 6 HA CA N C +SER 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA OG +1 2 HG OG CB CA +THR 5 +1 1 H N -C CA +1 5 HA CA N CB C +1 5 HB CB CA CG2 OG1 +3 4 HG2 CG2 CB CA +1 2 HG1 OG1 CB CA +LEU 6 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 5 HG CG CB CD1 CD2 +3 4 HD1 CD1 CG CB +3 4 HD2 CD2 CG CB +ILE 6 +1 1 H N -C CA +1 5 HA CA N CB C +1 5 HB CB CA CG2 CG1 +3 4 HG2 CG2 CB CA +2 6 HG1 CG1 CB CD +3 4 HD CD CG1 CB +VAL 5 +1 1 H N -C CA +1 5 HA CA N CB C +1 5 HB CB CA CG1 CG2 +3 4 HG1 CG1 CB CA +3 4 HG2 CG2 CB CA +ASN 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 3 HD2 ND2 CG CB +GLN 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 3 HE2 NE2 CD CG +ARG 8 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG NE +1 1 HE NE CD CZ +2 3 HH1 NH1 CZ NE +2 3 HH2 NH2 CZ NE +HID 6 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 ND1 CG CE1 +1 1 HE1 CE1 ND1 NE2 +1 1 HD2 CD2 CG NE2 +HIE 6 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HE1 CE1 ND1 NE2 +1 1 HE2 NE2 CE1 CD2 +1 1 HD2 CD2 CG NE2 +HIP 7 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 ND1 CG CE1 +1 1 HE1 CE1 ND1 NE2 +1 1 HE2 NE2 CE1 CD2 +1 1 HD2 CD2 CG NE2 +TRP 9 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG NE1 +1 1 HE1 NE1 CD1 CE2 +1 1 HZ2 CZ2 CE2 CH2 +1 1 HH2 CH2 CZ2 CZ3 +1 1 HZ3 CZ3 CH2 CE3 +1 1 HE3 CE3 CZ3 CD2 +PHE 8 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG CE1 +1 1 HE1 CE1 CD1 CZ +1 1 HZ CZ CE1 CE2 +1 1 HE2 CE2 CZ CD2 +1 1 HD2 CD2 CG CE2 +TYR 8 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG CE1 +1 1 HE1 CE1 CD1 CZ +1 2 HH OH CZ CE1 +1 1 HE2 CE2 CZ CD2 +1 1 HD2 CD2 CG CE2 +GLU 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +ASP 3 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +LYS 7 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG CE +2 6 HE CE CD NZ +3 4 HZ NZ CE CD +ORN 6 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG NE +3 4 HE NE CD CG +DAB 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB ND +3 4 HD ND CG CB +LYN 7 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG CE +2 6 HE CE CD NZ +2 3 HZ NZ CE CD +PRO 4 +2 6 HD CD N CG +2 6 HG CG CD CB +2 6 HB CB CG CA +1 5 HA CA N CB C +HYP 5 +2 6 HD2 CD2 N CG +1 5 HG CG CD2 OD1 CB +1 2 HD1 OD1 CG CD2 +2 6 HB CB CG CA +1 5 HA CA N CB C +CYS 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA SG +1 2 HG SG CB CA +CYM 3 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA SG +CYX 3 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA SG +CYS2 3 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA SG +MET 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB SD +3 4 HE CE SD CG +ASH 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 2 HD2 OD2 CG CB +GLH 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +1 2 HE2 OE2 CD CG +CALA 4 +1 1 H N -C CA +1 5 HA CA N CB C +3 4 HB CB CA N +1 1 OC1 C CA OC2 +CGLY 3 +1 1 H N -C CA +2 6 HA CA N C +1 1 OC1 C CA OC2 +CSER 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA OG +1 2 HG OG CB CA +1 1 OC1 C CA OC2 +CTHR 6 +1 1 H N -C CA +1 5 HA CA N CB C +1 5 HB CB CA CG2 OG1 +3 4 HG2 CG2 CB CA +1 2 HG1 OG1 CB CA +1 1 OC1 C CA OC2 +CLEU 7 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 5 HG CG CB CD1 CD2 +3 4 HD1 CD1 CG CB +3 4 HD2 CD2 CG CB +1 1 OC1 C CA OC2 +CILE 7 +1 1 H N -C CA +1 5 HA CA N CB C +1 5 HB CB CA CG2 CG1 +3 4 HG2 CG2 CB CA +2 6 HG1 CG1 CB CD +3 4 HD CD CG1 CB +1 1 OC1 C CA OC2 +CVAL 6 +1 1 H N -C CA +1 5 HA CA N CB C +1 5 HB CB CA CG1 CG2 +3 4 HG1 CG1 CB CA +3 4 HG2 CG2 CB CA +1 1 OC1 C CA OC2 +CASN 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 3 HD2 ND2 CG CB +1 1 OC1 C CA OC2 +CGLN 6 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 3 HE2 NE2 CD CG +1 1 OC1 C CA OC2 +CARG 9 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG NE +1 1 HE NE CD CZ +2 3 HH1 NH1 CZ NE +2 3 HH2 NH2 CZ NE +1 1 OC1 C CA OC2 +CHID 7 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 ND1 CG CE1 +1 1 HE1 CE1 ND1 NE2 +1 1 HD2 CD2 CG NE2 +1 1 OC1 C CA OC2 +CHIE 7 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HE1 CE1 ND1 NE2 +1 1 HE2 NE2 CE1 CD2 +1 1 HD2 CD2 CG NE2 +1 1 OC1 C CA OC2 +CHIP 8 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 ND1 CG CE1 +1 1 HE1 CE1 ND1 NE2 +1 1 HE2 NE2 CE1 CD2 +1 1 HD2 CD2 CG NE2 +1 1 OC1 C CA OC2 +CTRP 10 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG NE1 +1 1 HE1 NE1 CD1 CE2 +1 1 HZ2 CZ2 CE2 CH2 +1 1 HH2 CH2 CZ2 CZ3 +1 1 HZ3 CZ3 CH2 CE3 +1 1 HE3 CE3 CZ3 CD2 +1 1 OC1 C CA OC2 +CPHE 9 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG CE1 +1 1 HE1 CE1 CD1 CZ +1 1 HZ CZ CE1 CE2 +1 1 HE2 CE2 CZ CD2 +1 1 HD2 CD2 CG CE2 +1 1 OC1 C CA OC2 +CTYR 9 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG CE1 +1 1 HE1 CE1 CD1 CZ +1 2 HH OH CZ CE1 +1 1 HE2 CE2 CZ CD2 +1 1 HD2 CD2 CG CE2 +1 1 OC1 C CA OC2 +CGLU 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +1 1 OC1 C CA OC2 +CASP 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 OC1 C CA OC2 +CLYS 8 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG CE +2 6 HE CE CD NZ +3 4 HZ NZ CE CD +1 1 OC1 C CA OC2 +CPRO 5 +2 6 HD CD N CG +2 6 HG CG CD CB +2 6 HB CB CG CA +1 5 HA CA N CB C +1 1 OC1 C CA OC2 +CCYS 5 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA SG +1 2 HG SG CB CA +1 1 OC1 C CA OC2 +CCYX 4 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA SG +1 1 OC1 C CA OC2 +CMET 6 +1 1 H N -C CA +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB SD +3 4 HE CE SD CG +1 1 OC1 C CA OC2 +NALA 3 +3 4 H N CA CB +1 5 HA CA N CB C +3 4 HB CB CA N +NGLY 2 +3 4 H N CA C +2 6 HA CA N C +NSER 4 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA OG +1 2 HG OG CB CA +NTHR 5 +3 4 H N CA CB +1 5 HA CA N CB C +1 5 HB CB CA CG2 OG1 +3 4 HG2 CG2 CB CA +1 2 HG1 OG1 CB CA +NLEU 6 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 5 HG CG CB CD1 CD2 +3 4 HD1 CD1 CG CB +3 4 HD2 CD2 CG CB +NILE 6 +3 4 H N CA CB +1 5 HA CA N CB C +1 5 HB CB CA CG2 CG1 +3 4 HG2 CG2 CB CA +2 6 HG1 CG1 CB CD +3 4 HD CD CG1 CB +NVAL 5 +3 4 H N CA CB +1 5 HA CA N CB C +1 5 HB CB CA CG1 CG2 +3 4 HG1 CG1 CB CA +3 4 HG2 CG2 CB CA +NASN 4 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +2 3 HD2 ND2 CG CB +NGLN 5 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 3 HE2 NE2 CD CG +NARG 8 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG NE +1 1 HE NE CD CZ +2 3 HH1 NH1 CZ NE +2 3 HH2 NH2 CZ NE +NHID 6 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 ND1 CG CE1 +1 1 HE1 CE1 ND1 NE2 +1 1 HD2 CD2 CG NE2 +NHIE 6 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HE1 CE1 ND1 NE2 +1 1 HE2 NE2 CE1 CD2 +1 1 HD2 CD2 CG NE2 +NHIP 7 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 ND1 CG CE1 +1 1 HE1 CE1 ND1 NE2 +1 1 HE2 NE2 CE1 CD2 +1 1 HD2 CD2 CG NE2 +NTRP 9 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG NE1 +1 1 HE1 NE1 CD1 CE2 +1 1 HZ2 CZ2 CE2 CH2 +1 1 HH2 CH2 CZ2 CZ3 +1 1 HZ3 CZ3 CH2 CE3 +1 1 HE3 CE3 CZ3 CD2 +NPHE 8 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG CE1 +1 1 HE1 CE1 CD1 CZ +1 1 HZ CZ CE1 CE2 +1 1 HE2 CE2 CZ CD2 +1 1 HD2 CD2 CG CE2 +NTYR 8 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +1 1 HD1 CD1 CG CE1 +1 1 HE1 CE1 CD1 CZ +1 2 HH OH CZ CE1 +1 1 HE2 CE2 CZ CD2 +1 1 HD2 CD2 CG CE2 +NGLU 4 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +NASP 3 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +NLYS 7 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB CD +2 6 HD CD CG CE +2 6 HE CE CD NZ +3 4 HZ NZ CE CD +NPRO 5 +2 6 H N CA CD +2 6 HD CD N CG +2 6 HG CG CD CB +2 6 HB CB CG CA +1 5 HA CA N CB C +NCYS 4 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA SG +1 2 HG SG CB CA +NCYX 3 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA SG +NMET 5 +3 4 H N CA CB +1 5 HA CA N CB C +2 6 HB CB CA CG +2 6 HG CG CB SD +3 4 HE CE SD CG diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.n.tdb b/tests/test_files/assets/amber14sb.ff/aminoacids.n.tdb new file mode 100644 index 0000000..50d0742 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.n.tdb @@ -0,0 +1,3 @@ +; empty + + diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.r2b b/tests/test_files/assets/amber14sb.ff/aminoacids.r2b new file mode 100644 index 0000000..bba55ba --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.r2b @@ -0,0 +1,31 @@ +; rtp residue to rtp building block table +;GMX Force-field +; main N-ter C-ter 2-ter +ALA ALA NALA CALA - +ARG ARG NARG CARG - +ARGN - - - - +ASN ASN NASN CASN - +ASP ASP NASP CASP - +ASPH ASH - - - +CYS CYS NCYS CCYS - +CYS2 CYX NCYX CCYX - +GLN GLN NGLN CGLN - +QLN - - - - +GLU GLU NGLU CGLU - +GLY GLY NGLY CGLY - +GLUH GLH - - - +HISD HID NHID CHID - +HISE HIE NHIE CHIE - +HISH HIP NHIP CHIP - +ILE ILE NILE CILE - +LYSN LYN - - - +LYS LYS NLYS CLYS - +LEU LEU NLEU CLEU - +MET MET NMET CMET - +PHE PHE NPHE CPHE - +PRO PRO NPRO CPRO - +SER SER NSER CSER - +THR THR NTHR CTHR - +TRP TRP NTRP CTRP - +TYR TYR NTYR CTYR - +VAL VAL NVAL CVAL - diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.rtp b/tests/test_files/assets/amber14sb.ff/aminoacids.rtp new file mode 100644 index 0000000..81cddfb --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.rtp @@ -0,0 +1,3401 @@ +[ bondedtypes ] +; Col 1: Type of bond +; Col 2: Type of angles +; Col 3: Type of proper dihedrals +; Col 4: Type of improper dihedrals +; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. +; Col 6: Number of excluded neighbors for nonbonded interactions +; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 +; Col 8: Remove impropers over the same bond as a proper if it is 1 +; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih + 1 1 9 4 1 3 1 0 + +; now: water, ions, urea, terminal caps, AA's and terminal AA's + +; tip3p +[ HOH ] + [ atoms ] + OW OW -0.834 0 + HW1 HW 0.417 0 + HW2 HW 0.417 0 + [ bonds ] + OW HW1 + OW HW2 + +; tip4p +[ HO4 ] + [ atoms ] + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 + [ bonds ] + OW HW1 + OW HW2 + +[ IB+ ] ; big positive ion + [ atoms ] + IB IB 1.00000 1 + +[ CA ] + [ atoms ] + CA C0 2.00000 1 + +[ CL ] + [ atoms ] + CL Cl -1.00000 1 + +[ NA ] + [ atoms ] + NA Na 1.00000 1 + +[ MG ] + [ atoms ] + MG MG 2.00000 1 + +[ K ] + [ atoms ] + K K 1.00000 1 + +[ RB ] + [ atoms ] + RB Rb 1.00000 1 + +[ CS ] + [ atoms ] + CS Cs 1.00000 1 + +[ LI ] + [ atoms ] + LI Li 1.00000 1 + +[ ZN ] + [ atoms ] + ZN Zn 2.00000 1 + +[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell + [ atoms ] + C C 0.880229 1 + O O -0.613359 2 + N1 N -0.923545 3 + H11 H 0.395055 4 + H12 H 0.395055 5 + N2 N -0.923545 6 + H21 H 0.395055 7 + H22 H 0.395055 8 + [ bonds ] + C N1 + C N2 + C O + N1 H11 + N1 H12 + N2 H21 + N2 H22 + [ impropers ] + N1 N2 C O + C H11 N1 H12 + C H21 N2 H22 + +[ ACE ] + [ atoms ] + HH31 HC 0.11230 1 + CH3 CT -0.36620 2 + HH32 HC 0.11230 3 + HH33 HC 0.11230 4 + C C 0.59720 5 + O O -0.56790 6 + [ bonds ] + HH31 CH3 + CH3 HH32 + CH3 HH33 + CH3 C + C O + [ impropers ] + CH3 +N C O + +[ NME ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CH3 CT -0.14900 3 + HH31 H1 0.09760 4 + HH32 H1 0.09760 5 + HH33 H1 0.09760 6 + [ bonds ] + N H + N CH3 + CH3 HH31 + CH3 HH32 + CH3 HH33 + -C N + [ impropers ] + -C CH3 N H + +[ NHE ] + [ atoms ] + N N -0.46300 1 + H1 H 0.23150 2 + H2 H 0.23150 3 + [ bonds ] + N H1 + N H2 + -C N + [ impropers ] + -C H1 N H2 + +[ NH2 ] + [ atoms ] + N N -0.46300 1 + H1 H 0.23150 2 + H2 H 0.23150 3 + [ bonds ] + N H1 + N H2 + -C N + [ impropers ] + -C H1 N H2 + +; Next are non-terminal AA's + +[ ALA ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.03370 3 + HA H1 0.08230 4 + CB CT -0.18250 5 + HB1 HC 0.06030 6 + HB2 HC 0.06030 7 + HB3 HC 0.06030 8 + C C 0.59730 9 + O O -0.56790 10 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB HB3 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ GLY ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.02520 3 + HA1 H1 0.06980 4 + HA2 H1 0.06980 5 + C C 0.59730 6 + O O -0.56790 7 + [ bonds ] + N H + N CA + CA HA1 + CA HA2 + CA C + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ SER ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.02490 3 + HA H1 0.08430 4 + CB 2C 0.21170 5 + HB1 H1 0.03520 6 + HB2 H1 0.03520 7 + OG OH -0.65460 8 + HG HO 0.42750 9 + C C 0.59730 10 + O O -0.56790 11 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB OG + OG HG + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ THR ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.03890 3 + HA H1 0.10070 4 + CB 3C 0.36540 5 + HB H1 0.00430 6 + CG2 CT -0.24380 7 + HG21 HC 0.06420 8 + HG22 HC 0.06420 9 + HG23 HC 0.06420 10 + OG1 OH -0.67610 11 + HG1 HO 0.41020 12 + C C 0.59730 13 + O O -0.56790 14 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB + CB CG2 + CB OG1 + CG2 HG21 + CG2 HG22 + CG2 HG23 + OG1 HG1 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ LEU ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.05180 3 + HA H1 0.09220 4 + CB 2C -0.11020 5 + HB1 HC 0.04570 6 + HB2 HC 0.04570 7 + CG 3C 0.35310 8 + HG HC -0.03610 9 + CD1 CT -0.41210 10 + HD11 HC 0.10000 11 + HD12 HC 0.10000 12 + HD13 HC 0.10000 13 + CD2 CT -0.41210 14 + HD21 HC 0.10000 15 + HD22 HC 0.10000 16 + HD23 HC 0.10000 17 + C C 0.59730 18 + O O -0.56790 19 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG + CG CD1 + CG CD2 + CD1 HD11 + CD1 HD12 + CD1 HD13 + CD2 HD21 + CD2 HD22 + CD2 HD23 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ ILE ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.05970 3 + HA H1 0.08690 4 + CB 3C 0.13030 5 + HB HC 0.01870 6 + CG2 CT -0.32040 7 + HG21 HC 0.08820 8 + HG22 HC 0.08820 9 + HG23 HC 0.08820 10 + CG1 2C -0.04300 11 + HG11 HC 0.02360 12 + HG12 HC 0.02360 13 + CD CT -0.06600 14 + HD1 HC 0.01860 15 + HD2 HC 0.01860 16 + HD3 HC 0.01860 17 + C C 0.59730 18 + O O -0.56790 19 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB + CB CG2 + CB CG1 + CG2 HG21 + CG2 HG22 + CG2 HG23 + CG1 HG11 + CG1 HG12 + CG1 CD + CD HD1 + CD HD2 + CD HD3 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ VAL ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.08750 3 + HA H1 0.09690 4 + CB 3C 0.29850 5 + HB HC -0.02970 6 + CG1 CT -0.31920 7 + HG11 HC 0.07910 8 + HG12 HC 0.07910 9 + HG13 HC 0.07910 10 + CG2 CT -0.31920 11 + HG21 HC 0.07910 12 + HG22 HC 0.07910 13 + HG23 HC 0.07910 14 + C C 0.59730 15 + O O -0.56790 16 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB + CB CG1 + CB CG2 + CG1 HG11 + CG1 HG12 + CG1 HG13 + CG2 HG21 + CG2 HG22 + CG2 HG23 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ ASN ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.01430 3 + HA H1 0.10480 4 + CB 2C -0.20410 5 + HB1 HC 0.07970 6 + HB2 HC 0.07970 7 + CG C 0.71300 8 + OD1 O -0.59310 9 + ND2 N -0.91910 10 + HD21 H 0.41960 11 + HD22 H 0.41960 12 + C C 0.59730 13 + O O -0.56790 14 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG ND2 + ND2 HD21 + ND2 HD22 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +[ GLN ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.00310 3 + HA H1 0.08500 4 + CB 2C -0.00360 5 + HB1 HC 0.01710 6 + HB2 HC 0.01710 7 + CG 2C -0.06450 8 + HG1 HC 0.03520 9 + HG2 HC 0.03520 10 + CD C 0.69510 11 + OE1 O -0.60860 12 + NE2 N -0.94070 13 + HE21 H 0.42510 14 + HE22 H 0.42510 15 + C C 0.59730 16 + O O -0.56790 17 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD NE2 + NE2 HE21 + NE2 HE22 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +[ ARG ] + [ atoms ] + N N -0.34790 1 + H H 0.27470 2 + CA CX -0.26370 3 + HA H1 0.15600 4 + CB C8 -0.00070 5 + HB1 HC 0.03270 6 + HB2 HC 0.03270 7 + CG C8 0.03900 8 + HG1 HC 0.02850 9 + HG2 HC 0.02850 10 + CD C8 0.04860 11 + HD1 H1 0.06870 12 + HD2 H1 0.06870 13 + NE N2 -0.52950 14 + HE H 0.34560 15 + CZ CA 0.80760 16 + NH1 N2 -0.86270 17 + HH11 H 0.44780 18 + HH12 H 0.44780 19 + NH2 N2 -0.86270 20 + HH21 H 0.44780 21 + HH22 H 0.44780 22 + C C 0.73410 23 + O O -0.58940 24 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD NE + NE HE + NE CZ + CZ NH1 + CZ NH2 + NH1 HH11 + NH1 HH12 + NH2 HH21 + NH2 HH22 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + NE NH1 CZ NH2 + CD CZ NE HE + CZ HH11 NH1 HH12 + CZ HH21 NH2 HH22 + +[ HID ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.01880 3 + HA H1 0.08810 4 + CB CT -0.04620 5 + HB1 HC 0.04020 6 + HB2 HC 0.04020 7 + CG CC -0.02660 8 + ND1 NA -0.38110 9 + HD1 H 0.36490 10 + CE1 CR 0.20570 11 + HE1 H5 0.13920 12 + NE2 NB -0.57270 13 + CD2 CV 0.12920 14 + HD2 H4 0.11470 15 + C C 0.59730 16 + O O -0.56790 17 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 HD1 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 CD2 + CD2 HD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ HIE ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.05810 3 + HA H1 0.13600 4 + CB CT -0.00740 5 + HB1 HC 0.03670 6 + HB2 HC 0.03670 7 + CG CC 0.18680 8 + ND1 NB -0.54320 9 + CE1 CR 0.16350 10 + HE1 H5 0.14350 11 + NE2 NA -0.27950 12 + HE2 H 0.33390 13 + CD2 CW -0.22070 14 + HD2 H4 0.18620 15 + C C 0.59730 16 + O O -0.56790 17 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB2 + CB HB1 + CB CG + CG ND1 + CG CD2 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 HE2 + NE2 CD2 + CD2 HD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ HIP ] + [ atoms ] + N N -0.34790 1 + H H 0.27470 2 + CA CX -0.13540 3 + HA H1 0.12120 4 + CB CT -0.04140 5 + HB1 HC 0.08100 6 + HB2 HC 0.08100 7 + CG CC -0.00120 8 + ND1 NA -0.15130 9 + HD1 H 0.38660 10 + CE1 CR -0.01700 11 + HE1 H5 0.26810 12 + NE2 NA -0.17180 13 + HE2 H 0.39110 14 + CD2 CW -0.11410 15 + HD2 H4 0.23170 16 + C C 0.73410 17 + O O -0.58940 18 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 HD1 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 HE2 + NE2 CD2 + CD2 HD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ TRP ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.02750 3 + HA H1 0.11230 4 + CB CT -0.00500 5 + HB1 HC 0.03390 6 + HB2 HC 0.03390 7 + CG C* -0.14150 8 + CD1 CW -0.16380 9 + HD1 H4 0.20620 10 + NE1 NA -0.34180 11 + HE1 H 0.34120 12 + CE2 CN 0.13800 13 + CZ2 CA -0.26010 14 + HZ2 HA 0.15720 15 + CH2 CA -0.11340 16 + HH2 HA 0.14170 17 + CZ3 CA -0.19720 18 + HZ3 HA 0.14470 19 + CE3 CA -0.23870 20 + HE3 HA 0.17000 21 + CD2 CB 0.12430 22 + C C 0.59730 23 + O O -0.56790 24 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 NE1 + NE1 HE1 + NE1 CE2 + CE2 CZ2 + CE2 CD2 + CZ2 HZ2 + CZ2 CH2 + CH2 HH2 + CH2 CZ3 + CZ3 HZ3 + CZ3 CE3 + CE3 HE3 + CE3 CD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CG CB CD2 + +[ PHE ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.00240 3 + HA H1 0.09780 4 + CB CT -0.03430 5 + HB1 HC 0.02950 6 + HB2 HC 0.02950 7 + CG CA 0.01180 8 + CD1 CA -0.12560 9 + HD1 HA 0.13300 10 + CE1 CA -0.17040 11 + HE1 HA 0.14300 12 + CZ CA -0.10720 13 + HZ HA 0.12970 14 + CE2 CA -0.17040 15 + HE2 HA 0.14300 16 + CD2 CA -0.12560 17 + HD2 HA 0.13300 18 + C C 0.59730 19 + O O -0.56790 20 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 CE1 + CE1 HE1 + CE1 CZ + CZ HZ + CZ CE2 + CE2 HE2 + CE2 CD2 + CD2 HD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG CE2 CD2 HD2 + CZ CD2 CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +[ TYR ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.00140 3 + HA H1 0.08760 4 + CB CT -0.01520 5 + HB1 HC 0.02950 6 + HB2 HC 0.02950 7 + CG CA -0.00110 8 + CD1 CA -0.19060 9 + HD1 HA 0.16990 10 + CE1 CA -0.23410 11 + HE1 HA 0.16560 12 + CZ C 0.32260 13 + OH OH -0.55790 14 + HH HO 0.39920 15 + CE2 CA -0.23410 16 + HE2 HA 0.16560 17 + CD2 CA -0.19060 18 + HD2 HA 0.16990 19 + C C 0.59730 20 + O O -0.56790 21 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 CE1 + CE1 HE1 + CE1 CZ + CZ OH + CZ CE2 + OH HH + CE2 HE2 + CE2 CD2 + CD2 HD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG CE2 CD2 HD2 + CZ CD2 CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + +[ GLU ] + [ atoms ] + N N -0.51630 1 + H H 0.29360 2 + CA CX 0.03970 3 + HA H1 0.11050 4 + CB 2C 0.05600 5 + HB1 HC -0.01730 6 + HB2 HC -0.01730 7 + CG 2C 0.01360 8 + HG1 HC -0.04250 9 + HG2 HC -0.04250 10 + CD CO 0.80540 11 + OE1 O2 -0.81880 12 + OE2 O2 -0.81880 13 + C C 0.53660 14 + O O -0.58190 15 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD OE2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG OE1 CD OE2 + +[ ASP ] + [ atoms ] + N N -0.51630 1 + H H 0.29360 2 + CA CX 0.03810 3 + HA H1 0.08800 4 + CB 2C -0.03030 5 + HB1 HC -0.01220 6 + HB2 HC -0.01220 7 + CG CO 0.79940 8 + OD1 O2 -0.80140 9 + OD2 O2 -0.80140 10 + C C 0.53660 11 + O O -0.58190 12 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG OD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CB OD1 CG OD2 + +[ LYS ] + [ atoms ] + N N -0.34790 1 + H H 0.27470 2 + CA CX -0.24000 3 + HA H1 0.14260 4 + CB C8 -0.00940 5 + HB1 HC 0.03620 6 + HB2 HC 0.03620 7 + CG C8 0.01870 8 + HG1 HC 0.01030 9 + HG2 HC 0.01030 10 + CD C8 -0.04790 11 + HD1 HC 0.06210 12 + HD2 HC 0.06210 13 + CE C8 -0.01430 14 + HE1 HP 0.11350 15 + HE2 HP 0.11350 16 + NZ N3 -0.38540 17 + HZ1 H 0.34000 18 + HZ2 H 0.34000 19 + HZ3 H 0.34000 20 + C C 0.73410 21 + O O -0.58940 22 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD CE + CE HE1 + CE HE2 + CE NZ + NZ HZ1 + NZ HZ2 + NZ HZ3 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ ORN ] ; charges taken from amber99.prm of tinker 4.0 + [ atoms ] + N N -0.34790 1 + H H 0.27470 2 + CA CT -0.24000 3 + HA H1 0.14260 4 + CB CT 0.00990 5 + HB1 HC 0.03620 6 + HB2 HC 0.03620 7 + CG CT -0.02790 8 + HG1 HC 0.06210 9 + HG2 HC 0.06210 10 + CD CT -0.01430 11 + HD1 HP 0.11350 12 + HD2 HP 0.11350 13 + NE N3 -0.38540 14 + HE1 H 0.34000 15 + HE2 H 0.34000 16 + HE3 H 0.34000 17 + C C 0.73410 18 + O O -0.58940 19 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD NE + NE HE1 + NE HE2 + NE HE3 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ DAB ] ; sidechain charges fit to maintain heavy atom charge group trend LYS -> ORN -> DAB + [ atoms ] + N N -0.34790 1 + H H 0.27470 2 + CA CT -0.24000 3 + HA H1 0.14260 4 + CB CT 0.02920 5 + HB1 HC 0.07470 6 + HB2 HC 0.07470 7 + CG CT -0.01430 8 + HG1 HP 0.11350 9 + HG2 HP 0.11350 10 + ND N3 -0.38540 11 + HD1 H 0.34000 12 + HD2 H 0.34000 13 + HD3 H 0.34000 14 + C C 0.73410 15 + O O -0.58940 16 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG ND + ND HD1 + ND HD2 + ND HD3 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ LYN ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.07206 3 + HA H1 0.09940 4 + CB CT -0.04845 5 + HB1 HC 0.03400 6 + HB2 HC 0.03400 7 + CG CT 0.06612 8 + HG1 HC 0.01041 9 + HG2 HC 0.01041 10 + CD CT -0.03768 11 + HD1 HC 0.01155 12 + HD2 HC 0.01155 13 + CE CT 0.32604 14 + HE1 HP -0.03358 15 + HE2 HP -0.03358 16 + NZ N3 -1.03581 17 + HZ1 H 0.38604 18 + HZ2 H 0.38604 19 + C C 0.59730 20 + O O -0.56790 21 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD CE + CE HE1 + CE HE2 + CE NZ + NZ HZ1 + NZ HZ2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ PRO ] + [ atoms ] + N N -0.25480 1 + CD CT 0.01920 2 + HD1 H1 0.03910 3 + HD2 H1 0.03910 4 + CG CT 0.01890 5 + HG1 HC 0.02130 6 + HG2 HC 0.02130 7 + CB CT -0.00700 8 + HB1 HC 0.02530 9 + HB2 HC 0.02530 10 + CA CX -0.02660 11 + HA H1 0.06410 12 + C C 0.58960 13 + O O -0.57480 14 + [ bonds ] + N CD + N CA + CD HD1 + CD HD2 + CD CG + CG HG1 + CG HG2 + CG CB + CB HB1 + CB HB2 + CB CA + CA HA + CA C + C O + -C N + [ impropers ] + CA +N C O + -C CD N CA + +[ HYP ] ; S Park, R J Radmer, T E Klein & V S Pande (submitted). + [ atoms ] + N N -0.25480 1 + CD2 CT 0.05950 2 + HD21 H1 0.07000 3 + HD22 H1 0.07000 4 + CG CT 0.04000 5 + HG H1 0.04160 6 + OD1 OH -0.61340 7 + HD1 HO 0.38510 8 + CB CT 0.02030 9 + HB1 HC 0.04260 10 + HB2 HC 0.04260 11 + CA CX 0.00470 12 + HA H1 0.07700 13 + C C 0.58960 14 + O O -0.57480 15 + [ bonds ] + N CD2 + N CA + CD2 HD21 + CD2 HD22 + CD2 CG + CG HG + CG OD1 + CG CB + OD1 HD1 + CB HB1 + CB HB2 + CB CA + CA HA + CA C + C O + -C N + [ impropers ] + CA +N C O + -C CD2 N CA + +[ CYS ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.02130 3 + HA H1 0.11240 4 + CB 2C -0.12310 5 + HB1 H1 0.11120 6 + HB2 H1 0.11120 7 + SG SH -0.31190 8 + HG HS 0.19330 9 + C C 0.59730 10 + O O -0.56790 11 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB SG + SG HG + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ CYM ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.03510 3 + HA H1 0.05080 4 + CB CT -0.24130 5 + HB1 H1 0.11220 6 + HB2 H1 0.11220 7 + SG SH -0.88440 8 + C C 0.59730 9 + O O -0.56790 10 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB SG + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ CYX ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.04290 3 + HA H1 0.07660 4 + CB 2C -0.07900 5 + HB1 H1 0.09100 6 + HB2 H1 0.09100 7 + SG S -0.10810 8 + C C 0.59730 9 + O O -0.56790 10 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB SG + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +[ MET ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX -0.02370 3 + HA H1 0.08800 4 + CB 2C 0.03420 5 + HB1 HC 0.02410 6 + HB2 HC 0.02410 7 + CG 2C 0.00180 8 + HG1 H1 0.04400 9 + HG2 H1 0.04400 10 + SD S -0.27370 11 + CE CT -0.05360 12 + HE1 H1 0.06840 13 + HE2 H1 0.06840 14 + HE3 H1 0.06840 15 + C C 0.59730 16 + O O -0.56790 17 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG SD + SD CE + CE HE1 + CE HE2 + CE HE3 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + +; non-terminal acidic AA's + +[ ASH ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.03410 3 + HA H1 0.08640 4 + CB 2C -0.03160 5 + HB1 HC 0.04880 6 + HB2 HC 0.04880 7 + CG C 0.64620 8 + OD1 O -0.55540 9 + OD2 OH -0.63760 10 + HD2 HO 0.47470 11 + C C 0.59730 12 + O O -0.56790 13 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG OD2 + OD2 HD2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CB OD1 CG OD2 + + +[ GLH ] + [ atoms ] + N N -0.41570 1 + H H 0.27190 2 + CA CX 0.01450 3 + HA H1 0.07790 4 + CB 2C -0.00710 5 + HB1 HC 0.02560 6 + HB2 HC 0.02560 7 + CG 2C -0.01740 8 + HG1 HC 0.04300 9 + HG2 HC 0.04300 10 + CD C 0.68010 11 + OE1 O -0.58380 12 + OE2 OH -0.65110 13 + HE2 HO 0.46410 14 + C C 0.59730 15 + O O -0.56790 16 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD OE2 + OE2 HE2 + C O + -C N + [ impropers ] + -C CA N H + CA +N C O + CG OE1 CD OE2 + +; C-terminal AA's + +[ CALA ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.17470 3 + HA H1 0.10670 4 + CB CT -0.20930 5 + HB1 HC 0.07640 6 + HB2 HC 0.07640 7 + HB3 HC 0.07640 8 + C C 0.77310 9 + OC1 O2 -0.80550 10 + OC2 O2 -0.80550 11 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB HB3 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CGLY ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.24930 3 + HA1 H1 0.10560 4 + HA2 H1 0.10560 5 + C C 0.72310 6 + OC1 O2 -0.78550 7 + OC2 O2 -0.78550 8 + [ bonds ] + N H + N CA + CA HA1 + CA HA2 + CA C + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CSER ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.27220 3 + HA H1 0.13040 4 + CB 2C 0.11230 5 + HB1 H1 0.08130 6 + HB2 H1 0.08130 7 + OG OH -0.65140 8 + HG HO 0.44740 9 + C C 0.81130 10 + OC1 O2 -0.81320 11 + OC2 O2 -0.81320 12 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB OG + OG HG + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CTHR ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.24200 3 + HA H1 0.12070 4 + CB 3C 0.30250 5 + HB H1 0.00780 6 + CG2 CT -0.18530 7 + HG21 HC 0.05860 8 + HG22 HC 0.05860 9 + HG23 HC 0.05860 10 + OG1 OH -0.64960 11 + HG1 HO 0.41190 12 + C C 0.78100 13 + OC1 O2 -0.80440 14 + OC2 O2 -0.80440 15 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB + CB CG2 + CB OG1 + CG2 HG21 + CG2 HG22 + CG2 HG23 + OG1 HG1 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CLEU ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.28470 3 + HA H1 0.13460 4 + CB 2C -0.24690 5 + HB1 HC 0.09740 6 + HB2 HC 0.09740 7 + CG 3C 0.37060 8 + HG HC -0.03740 9 + CD1 CT -0.41630 10 + HD11 HC 0.10380 11 + HD12 HC 0.10380 12 + HD13 HC 0.10380 13 + CD2 CT -0.41630 14 + HD21 HC 0.10380 15 + HD22 HC 0.10380 16 + HD23 HC 0.10380 17 + C C 0.83260 18 + OC1 O2 -0.81990 19 + OC2 O2 -0.81990 20 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG + CG CD1 + CG CD2 + CD1 HD11 + CD1 HD12 + CD1 HD13 + CD2 HD21 + CD2 HD22 + CD2 HD23 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CILE ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.31000 3 + HA H1 0.13750 4 + CB 3C 0.03630 5 + HB HC 0.07660 6 + CG2 CT -0.34980 7 + HG21 HC 0.10210 8 + HG22 HC 0.10210 9 + HG23 HC 0.10210 10 + CG1 2C -0.03230 11 + HG11 HC 0.03210 12 + HG12 HC 0.03210 13 + CD CT -0.06990 14 + HD1 HC 0.01960 15 + HD2 HC 0.01960 16 + HD3 HC 0.01960 17 + C C 0.83430 18 + OC1 O2 -0.81900 19 + OC2 O2 -0.81900 20 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB + CB CG2 + CB CG1 + CG2 HG21 + CG2 HG22 + CG2 HG23 + CG1 HG11 + CG1 HG12 + CG1 CD + CD HD1 + CD HD2 + CD HD3 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CVAL ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.34380 3 + HA H1 0.14380 4 + CB 3C 0.19400 5 + HB HC 0.03080 6 + CG1 CT -0.30640 7 + HG11 HC 0.08360 8 + HG12 HC 0.08360 9 + HG13 HC 0.08360 10 + CG2 CT -0.30640 11 + HG21 HC 0.08360 12 + HG22 HC 0.08360 13 + HG23 HC 0.08360 14 + C C 0.83500 15 + OC1 O2 -0.81730 16 + OC2 O2 -0.81730 17 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB + CB CG1 + CB CG2 + CG1 HG11 + CG1 HG12 + CG1 HG13 + CG2 HG21 + CG2 HG22 + CG2 HG23 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CASN ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.20800 3 + HA H1 0.13580 4 + CB 2C -0.22990 5 + HB1 HC 0.10230 6 + HB2 HC 0.10230 7 + CG C 0.71530 8 + OD1 O -0.60100 9 + ND2 N -0.90840 10 + HD21 H 0.41500 11 + HD22 H 0.41500 12 + C C 0.80500 13 + OC1 O2 -0.81470 14 + OC2 O2 -0.81470 15 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG ND2 + ND2 HD21 + ND2 HD22 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +[ CGLN ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.22480 3 + HA H1 0.12320 4 + CB 2C -0.06640 5 + HB1 HC 0.04520 6 + HB2 HC 0.04520 7 + CG 2C -0.02100 8 + HG1 HC 0.02030 9 + HG2 HC 0.02030 10 + CD C 0.70930 11 + OE1 O -0.60980 12 + NE2 N -0.95740 13 + HE21 H 0.43040 14 + HE22 H 0.43040 15 + C C 0.77750 16 + OC1 O2 -0.80420 17 + OC2 O2 -0.80420 18 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD NE2 + NE2 HE21 + NE2 HE22 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +[ CARG ] + [ atoms ] + N N -0.34810 1 + H H 0.27640 2 + CA CX -0.30680 3 + HA H1 0.14470 4 + CB C8 -0.03740 5 + HB1 HC 0.03710 6 + HB2 HC 0.03710 7 + CG C8 0.07440 8 + HG1 HC 0.01850 9 + HG2 HC 0.01850 10 + CD C8 0.11140 11 + HD1 H1 0.04680 12 + HD2 H1 0.04680 13 + NE N2 -0.55640 14 + HE H 0.34790 15 + CZ CA 0.83680 16 + NH1 N2 -0.87370 17 + HH11 H 0.44930 18 + HH12 H 0.44930 19 + NH2 N2 -0.87370 20 + HH21 H 0.44930 21 + HH22 H 0.44930 22 + C C 0.85570 23 + OC1 O2 -0.82660 24 + OC2 O2 -0.82660 25 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD NE + NE HE + NE CZ + CZ NH1 + CZ NH2 + NH1 HH11 + NH1 HH12 + NH2 HH21 + NH2 HH22 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + NE NH1 CZ NH2 + CD CZ NE HE + CZ HH11 NH1 HH12 + CZ HH21 NH2 HH22 + +[ CHID ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.17390 3 + HA H1 0.11000 4 + CB CT -0.10460 5 + HB1 HC 0.05650 6 + HB2 HC 0.05650 7 + CG CC 0.02930 8 + ND1 NA -0.38920 9 + HD1 H 0.37550 10 + CE1 CR 0.19250 11 + HE1 H5 0.14180 12 + NE2 NB -0.56290 13 + CD2 CV 0.10010 14 + HD2 H4 0.12410 15 + C C 0.76150 16 + OC1 O2 -0.80160 17 + OC2 O2 -0.80160 18 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 HD1 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 CD2 + CD2 HD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ CHIE ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.26990 3 + HA H1 0.16500 4 + CB CT -0.10680 5 + HB1 HC 0.06200 6 + HB2 HC 0.06200 7 + CG CC 0.27240 8 + ND1 NB -0.55170 9 + CE1 CR 0.15580 10 + HE1 H5 0.14480 11 + NE2 NA -0.26700 12 + HE2 H 0.33190 13 + CD2 CW -0.25880 14 + HD2 H4 0.19570 15 + C C 0.79160 16 + OC1 O2 -0.80650 17 + OC2 O2 -0.80650 18 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 HE2 + NE2 CD2 + CD2 HD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ CHIP ] + [ atoms ] + N N -0.34810 1 + H H 0.27640 2 + CA CX -0.14450 3 + HA H1 0.11150 4 + CB CT -0.08000 5 + HB1 HC 0.08680 6 + HB2 HC 0.08680 7 + CG CC 0.02980 8 + ND1 NA -0.15010 9 + HD1 H 0.38830 10 + CE1 CR -0.02510 11 + HE1 H5 0.26940 12 + NE2 NA -0.16830 13 + HE2 H 0.39130 14 + CD2 CW -0.12560 15 + HD2 H4 0.23360 16 + C C 0.80320 17 + OC1 O2 -0.81770 18 + OC2 O2 -0.81770 19 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 HD1 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 HE2 + NE2 CD2 + CD2 HD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ CTRP ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.20840 3 + HA H1 0.12720 4 + CB CT -0.07420 5 + HB1 HC 0.04970 6 + HB2 HC 0.04970 7 + CG C* -0.07960 8 + CD1 CW -0.18080 9 + HD1 H4 0.20430 10 + NE1 NA -0.33160 11 + HE1 H 0.34130 12 + CE2 CN 0.12220 13 + CZ2 CA -0.25940 14 + HZ2 HA 0.15670 15 + CH2 CA -0.10200 16 + HH2 HA 0.14010 17 + CZ3 CA -0.22870 18 + HZ3 HA 0.15070 19 + CE3 CA -0.18370 20 + HE3 HA 0.14910 21 + CD2 CB 0.10780 22 + C C 0.76580 23 + OC1 O2 -0.80110 24 + OC2 O2 -0.80110 25 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 NE1 + NE1 HE1 + NE1 CE2 + CE2 CZ2 + CE2 CD2 + CZ2 HZ2 + CZ2 CH2 + CH2 HH2 + CH2 CZ3 + CZ3 HZ3 + CZ3 CE3 + CE3 HE3 + CE3 CD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CG CB CD2 + +[ CPHE ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.18250 3 + HA H1 0.10980 4 + CB CT -0.09590 5 + HB1 HC 0.04430 6 + HB2 HC 0.04430 7 + CG CA 0.05520 8 + CD1 CA -0.13000 9 + HD1 HA 0.14080 10 + CE1 CA -0.18470 11 + HE1 HA 0.14610 12 + CZ CA -0.09440 13 + HZ HA 0.12800 14 + CE2 CA -0.18470 15 + HE2 HA 0.14610 16 + CD2 CA -0.13000 17 + HD2 HA 0.14080 18 + C C 0.76600 19 + OC1 O2 -0.80260 20 + OC2 O2 -0.80260 21 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 CE1 + CE1 HE1 + CE1 CZ + CZ HZ + CZ CE2 + CE2 HE2 + CE2 CD2 + CD2 HD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CG CE2 CD2 HD2 + CZ CD2 CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +[ CTYR ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.20150 3 + HA H1 0.10920 4 + CB CT -0.07520 5 + HB1 HC 0.04900 6 + HB2 HC 0.04900 7 + CG CA 0.02430 8 + CD1 CA -0.19220 9 + HD1 HA 0.17800 10 + CE1 CA -0.24580 11 + HE1 HA 0.16730 12 + CZ C 0.33950 13 + OH OH -0.56430 14 + HH HO 0.40170 15 + CE2 CA -0.24580 16 + HE2 HA 0.16730 17 + CD2 CA -0.19220 18 + HD2 HA 0.17800 19 + C C 0.78170 20 + OC1 O2 -0.80700 21 + OC2 O2 -0.80700 22 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 CE1 + CE1 HE1 + CE1 CZ + CZ OH + CZ CE2 + OH HH + CE2 HE2 + CE2 CD2 + CD2 HD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CG CE2 CD2 HD2 + CZ CD2 CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + +[ CGLU ] + [ atoms ] + N N -0.51920 1 + H H 0.30550 2 + CA CX -0.20590 3 + HA H1 0.13990 4 + CB 2C 0.00710 5 + HB1 HC -0.00780 6 + HB2 HC -0.00780 7 + CG 2C 0.06750 8 + HG1 HC -0.05480 9 + HG2 HC -0.05480 10 + CD CO 0.81830 11 + OE1 O2 -0.82200 12 + OE2 O2 -0.82200 13 + C C 0.74200 14 + OC1 O2 -0.79300 15 + OC2 O2 -0.79300 16 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD OE2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CG OE1 CD OE2 + +[ CASP ] + [ atoms ] + N N -0.51920 1 + H H 0.30550 2 + CA CX -0.18170 3 + HA H1 0.10460 4 + CB 2C -0.06770 5 + HB1 HC -0.02120 6 + HB2 HC -0.02120 7 + CG CO 0.88510 8 + OD1 O2 -0.81620 9 + OD2 O2 -0.81620 10 + C C 0.72560 11 + OC1 O2 -0.78870 12 + OC2 O2 -0.78870 13 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG OD2 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + CB OD1 CG OD2 + +[ CLYS ] + [ atoms ] + N N -0.34810 1 + H H 0.27640 2 + CA CX -0.29030 3 + HA H1 0.14380 4 + CB C8 -0.05380 5 + HB1 HC 0.04820 6 + HB2 HC 0.04820 7 + CG C8 0.02270 8 + HG1 HC 0.01340 9 + HG2 HC 0.01340 10 + CD C8 -0.03920 11 + HD1 HC 0.06110 12 + HD2 HC 0.06110 13 + CE C8 -0.01760 14 + HE1 HP 0.11210 15 + HE2 HP 0.11210 16 + NZ N3 -0.37410 17 + HZ1 H 0.33740 18 + HZ2 H 0.33740 19 + HZ3 H 0.33740 20 + C C 0.84880 21 + OC1 O2 -0.82520 22 + OC2 O2 -0.82520 23 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD CE + CE HE1 + CE HE2 + CE NZ + NZ HZ1 + NZ HZ2 + NZ HZ3 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CPRO ] + [ atoms ] + N N -0.28020 1 + CD CT 0.04340 2 + HD1 H1 0.03310 3 + HD2 H1 0.03310 4 + CG CT 0.04660 5 + HG1 HC 0.01720 6 + HG2 HC 0.01720 7 + CB CT -0.05430 8 + HB1 HC 0.03810 9 + HB2 HC 0.03810 10 + CA CX -0.13360 11 + HA H1 0.07760 12 + C C 0.66310 13 + OC1 O2 -0.76970 14 + OC2 O2 -0.76970 15 + [ bonds ] + N CD + N CA + CD HD1 + CD HD2 + CD CG + CG HG1 + CG HG2 + CG CB + CB HB1 + CB HB2 + CB CA + CA HA + CA C + C OC1 + C OC2 + -C N + [ impropers ] + CA OC1 C OC2 + -C CD N CA + +[ CCYS ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.16350 3 + HA H1 0.13960 4 + CB 2C -0.19960 5 + HB1 H1 0.14370 6 + HB2 H1 0.14370 7 + SG SH -0.31020 8 + HG HS 0.20680 9 + C C 0.74970 10 + OC1 O2 -0.79810 11 + OC2 O2 -0.79810 12 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB SG + SG HG + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CCYX ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.13180 3 + HA H1 0.09380 4 + CB 2C -0.19430 5 + HB1 H1 0.12280 6 + HB2 H1 0.12280 7 + SG S -0.05290 8 + C C 0.76180 9 + OC1 O2 -0.80410 10 + OC2 O2 -0.80410 11 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB SG + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +[ CMET ] + [ atoms ] + N N -0.38210 1 + H H 0.26810 2 + CA CX -0.25970 3 + HA H1 0.12770 4 + CB 2C -0.02360 5 + HB1 HC 0.04800 6 + HB2 HC 0.04800 7 + CG 2C 0.04920 8 + HG1 H1 0.03170 9 + HG2 H1 0.03170 10 + SD S -0.26920 11 + CE CT -0.03760 12 + HE1 H1 0.06250 13 + HE2 H1 0.06250 14 + HE3 H1 0.06250 15 + C C 0.80130 16 + OC1 O2 -0.81050 17 + OC2 O2 -0.81050 18 + [ bonds ] + N H + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG SD + SD CE + CE HE1 + CE HE2 + CE HE3 + C OC1 + C OC2 + -C N + [ impropers ] + -C CA N H + CA OC1 C OC2 + +; N-terminal AA's + +[ NALA ] + [ atoms ] + N N3 0.14140 1 + H1 H 0.19970 2 + H2 H 0.19970 3 + H3 H 0.19970 4 + CA CX 0.09620 5 + HA HP 0.08890 6 + CB CT -0.05970 7 + HB1 HC 0.03000 8 + HB2 HC 0.03000 9 + HB3 HC 0.03000 10 + C C 0.61630 11 + O O -0.57220 12 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB HB3 + C O + C +N + [ impropers ] + CA +N C O + +[ NGLY ] + [ atoms ] + N N3 0.29430 1 + H1 H 0.16420 2 + H2 H 0.16420 3 + H3 H 0.16420 4 + CA CX -0.01000 5 + HA1 HP 0.08950 6 + HA2 HP 0.08950 7 + C C 0.61630 8 + O O -0.57220 9 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA1 + CA HA2 + CA C + C O + C +N + [ impropers ] + CA +N C O + +[ NSER ] + [ atoms ] + N N3 0.18490 1 + H1 H 0.18980 2 + H2 H 0.18980 3 + H3 H 0.18980 4 + CA CX 0.05670 5 + HA HP 0.07820 6 + CB 2C 0.25960 7 + HB1 H1 0.02730 8 + HB2 H1 0.02730 9 + OG OH -0.67140 10 + HG HO 0.42390 11 + C C 0.61630 12 + O O -0.57220 13 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB OG + OG HG + C O + C +N + [ impropers ] + CA +N C O + +[ NTHR ] + [ atoms ] + N N3 0.18120 1 + H1 H 0.19340 2 + H2 H 0.19340 3 + H3 H 0.19340 4 + CA CX 0.00340 5 + HA HP 0.10870 6 + CB 3C 0.45140 7 + HB H1 -0.03230 8 + CG2 CT -0.25540 9 + HG21 HC 0.06270 10 + HG22 HC 0.06270 11 + HG23 HC 0.06270 12 + OG1 OH -0.67640 13 + HG1 HO 0.40700 14 + C C 0.61630 15 + O O -0.57220 16 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB + CB CG2 + CB OG1 + CG2 HG21 + CG2 HG22 + CG2 HG23 + OG1 HG1 + C O + C +N + [ impropers ] + CA +N C O + +[ NLEU ] + [ atoms ] + N N3 0.10100 1 + H1 H 0.21480 2 + H2 H 0.21480 3 + H3 H 0.21480 4 + CA CX 0.01040 5 + HA HP 0.10530 6 + CB 2C -0.02440 7 + HB1 HC 0.02560 8 + HB2 HC 0.02560 9 + CG 3C 0.34210 10 + HG HC -0.03800 11 + CD1 CT -0.41060 12 + HD11 HC 0.09800 13 + HD12 HC 0.09800 14 + HD13 HC 0.09800 15 + CD2 CT -0.41040 16 + HD21 HC 0.09800 17 + HD22 HC 0.09800 18 + HD23 HC 0.09800 19 + C C 0.61230 20 + O O -0.57130 21 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG + CG CD1 + CG CD2 + CD1 HD11 + CD1 HD12 + CD1 HD13 + CD2 HD21 + CD2 HD22 + CD2 HD23 + C O + C +N + [ impropers ] + CA +N C O + +[ NILE ] + [ atoms ] + N N3 0.03110 1 + H1 H 0.23290 2 + H2 H 0.23290 3 + H3 H 0.23290 4 + CA CX 0.02570 5 + HA HP 0.10310 6 + CB 3C 0.18850 7 + HB HC 0.02130 8 + CG2 CT -0.37200 9 + HG21 HC 0.09470 10 + HG22 HC 0.09470 11 + HG23 HC 0.09470 12 + CG1 2C -0.03870 13 + HG11 HC 0.02010 14 + HG12 HC 0.02010 15 + CD CT -0.09080 16 + HD1 HC 0.02260 17 + HD2 HC 0.02260 18 + HD3 HC 0.02260 19 + C C 0.61230 20 + O O -0.57130 21 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB + CB CG2 + CB CG1 + CG2 HG21 + CG2 HG22 + CG2 HG23 + CG1 HG11 + CG1 HG12 + CG1 CD + CD HD1 + CD HD2 + CD HD3 + C O + C +N + [ impropers ] + CA +N C O + +[ NVAL ] + [ atoms ] + N N3 0.05770 1 + H1 H 0.22720 2 + H2 H 0.22720 3 + H3 H 0.22720 4 + CA CX -0.00540 5 + HA HP 0.10930 6 + CB 3C 0.31960 7 + HB HC -0.02210 8 + CG1 CT -0.31290 9 + HG11 HC 0.07350 10 + HG12 HC 0.07350 11 + HG13 HC 0.07350 12 + CG2 CT -0.31290 13 + HG21 HC 0.07350 14 + HG22 HC 0.07350 15 + HG23 HC 0.07350 16 + C C 0.61630 17 + O O -0.57220 18 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB + CB CG1 + CB CG2 + CG1 HG11 + CG1 HG12 + CG1 HG13 + CG2 HG21 + CG2 HG22 + CG2 HG23 + C O + C +N + [ impropers ] + CA +N C O + +[ NASN ] + [ atoms ] + N N3 0.18010 1 + H1 H 0.19210 2 + H2 H 0.19210 3 + H3 H 0.19210 4 + CA CX 0.03680 5 + HA HP 0.12310 6 + CB 2C -0.02830 7 + HB1 HC 0.05150 8 + HB2 HC 0.05150 9 + CG C 0.58330 10 + OD1 O -0.57440 11 + ND2 N -0.86340 12 + HD21 H 0.40970 13 + HD22 H 0.40970 14 + C C 0.61630 15 + O O -0.57220 16 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG ND2 + ND2 HD21 + ND2 HD22 + C O + C +N + [ impropers ] + CA +N C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +[ NGLN ] + [ atoms ] + N N3 0.14930 1 + H1 H 0.19960 2 + H2 H 0.19960 3 + H3 H 0.19960 4 + CA CX 0.05360 5 + HA HP 0.10150 6 + CB 2C 0.06510 7 + HB1 HC 0.00500 8 + HB2 HC 0.00500 9 + CG 2C -0.09030 10 + HG1 HC 0.03310 11 + HG2 HC 0.03310 12 + CD C 0.73540 13 + OE1 O -0.61330 14 + NE2 N -1.00310 15 + HE21 H 0.44290 16 + HE22 H 0.44290 17 + C C 0.61230 18 + O O -0.57130 19 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD NE2 + NE2 HE21 + NE2 HE22 + C O + C +N + [ impropers ] + CA +N C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +[ NARG ] + [ atoms ] + N N3 0.13050 1 + H1 H 0.20830 2 + H2 H 0.20830 3 + H3 H 0.20830 4 + CA CX -0.02230 5 + HA HP 0.12420 6 + CB C8 0.01180 7 + HB1 HC 0.02260 8 + HB2 HC 0.02260 9 + CG C8 0.02360 10 + HG1 HC 0.03090 11 + HG2 HC 0.03090 12 + CD C8 0.09350 13 + HD1 H1 0.05270 14 + HD2 H1 0.05270 15 + NE N2 -0.56500 16 + HE H 0.35920 17 + CZ CA 0.82810 18 + NH1 N2 -0.86930 19 + HH11 H 0.44940 20 + HH12 H 0.44940 21 + NH2 N2 -0.86930 22 + HH21 H 0.44940 23 + HH22 H 0.44940 24 + C C 0.72140 25 + O O -0.60130 26 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD NE + NE HE + NE CZ + CZ NH1 + CZ NH2 + NH1 HH11 + NH1 HH12 + NH2 HH21 + NH2 HH22 + C O + C +N + [ impropers ] + CA +N C O + NE NH1 CZ NH2 + CD CZ NE HE + CZ HH11 NH1 HH12 + CZ HH21 NH2 HH22 + +[ NHID ] + [ atoms ] + N N3 0.15420 1 + H1 H 0.19630 2 + H2 H 0.19630 3 + H3 H 0.19630 4 + CA CX 0.09640 5 + HA HP 0.09580 6 + CB CT 0.02590 7 + HB1 HC 0.02090 8 + HB2 HC 0.02090 9 + CG CC -0.03990 10 + ND1 NA -0.38190 11 + HD1 H 0.36320 12 + CE1 CR 0.21270 13 + HE1 H5 0.13850 14 + NE2 NB -0.57110 15 + CD2 CV 0.10460 16 + HD2 H4 0.12990 17 + C C 0.61230 18 + O O -0.57130 19 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 HD1 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 CD2 + CD2 HD2 + C O + C +N + [ impropers ] + CA +N C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ NHIE ] + [ atoms ] + N N3 0.14720 1 + H1 H 0.20160 2 + H2 H 0.20160 3 + H3 H 0.20160 4 + CA CX 0.02360 5 + HA HP 0.13800 6 + CB CT 0.04890 7 + HB1 HC 0.02230 8 + HB2 HC 0.02230 9 + CG CC 0.17400 10 + ND1 NB -0.55790 11 + CE1 CR 0.18040 12 + HE1 H5 0.13970 13 + NE2 NA -0.27810 14 + HE2 H 0.33240 15 + CD2 CW -0.23490 16 + HD2 H4 0.19630 17 + C C 0.61230 18 + O O -0.57130 19 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 HE2 + NE2 CD2 + CD2 HD2 + C O + C +N + [ impropers ] + CA +N C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ NHIP ] + [ atoms ] + N N3 0.25600 1 + H1 H 0.17040 2 + H2 H 0.17040 3 + H3 H 0.17040 4 + CA CX 0.05810 5 + HA HP 0.10470 6 + CB CT 0.04840 7 + HB1 HC 0.05310 8 + HB2 HC 0.05310 9 + CG CC -0.02360 10 + ND1 NA -0.15100 11 + HD1 H 0.38210 12 + CE1 CR -0.00110 13 + HE1 H5 0.26450 14 + NE2 NA -0.17390 15 + HE2 H 0.39210 16 + CD2 CW -0.14330 17 + HD2 H4 0.24950 18 + C C 0.72140 19 + O O -0.60130 20 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG ND1 + CG CD2 + ND1 HD1 + ND1 CE1 + CE1 HE1 + CE1 NE2 + NE2 HE2 + NE2 CD2 + CD2 HD2 + C O + C +N + [ impropers ] + CA +N C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +[ NTRP ] + [ atoms ] + N N3 0.19130 1 + H1 H 0.18880 2 + H2 H 0.18880 3 + H3 H 0.18880 4 + CA CX 0.04210 5 + HA HP 0.11620 6 + CB CT 0.05430 7 + HB1 HC 0.02220 8 + HB2 HC 0.02220 9 + CG C* -0.16540 10 + CD1 CW -0.17880 11 + HD1 H4 0.21950 12 + NE1 NA -0.34440 13 + HE1 H 0.34120 14 + CE2 CN 0.15750 15 + CZ2 CA -0.27100 16 + HZ2 HA 0.15890 17 + CH2 CA -0.10800 18 + HH2 HA 0.14110 19 + CZ3 CA -0.20340 20 + HZ3 HA 0.14580 21 + CE3 CA -0.22650 22 + HE3 HA 0.16460 23 + CD2 CB 0.11320 24 + C C 0.61230 25 + O O -0.57130 26 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 NE1 + NE1 HE1 + NE1 CE2 + CE2 CZ2 + CE2 CD2 + CZ2 HZ2 + CZ2 CH2 + CH2 HH2 + CH2 CZ3 + CZ3 HZ3 + CZ3 CE3 + CE3 HE3 + CE3 CD2 + C O + C +N + [ impropers ] + CA +N C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CG CB CD2 + +[ NPHE ] + [ atoms ] + N N3 0.17370 1 + H1 H 0.19210 2 + H2 H 0.19210 3 + H3 H 0.19210 4 + CA CX 0.07330 5 + HA HP 0.10410 6 + CB CT 0.03300 7 + HB1 HC 0.01040 8 + HB2 HC 0.01040 9 + CG CA 0.00310 10 + CD1 CA -0.13920 11 + HD1 HA 0.13740 12 + CE1 CA -0.16020 13 + HE1 HA 0.14330 14 + CZ CA -0.12080 15 + HZ HA 0.13290 16 + CE2 CA -0.16030 17 + HE2 HA 0.14330 18 + CD2 CA -0.13910 19 + HD2 HA 0.13740 20 + C C 0.61230 21 + O O -0.57130 22 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 CE1 + CE1 HE1 + CE1 CZ + CZ HZ + CZ CE2 + CE2 HE2 + CE2 CD2 + CD2 HD2 + C O + C +N + [ impropers ] + CA +N C O + CG CE2 CD2 HD2 + CZ CD2 CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +[ NTYR ] + [ atoms ] + N N3 0.19400 1 + H1 H 0.18730 2 + H2 H 0.18730 3 + H3 H 0.18730 4 + CA CX 0.05700 5 + HA HP 0.09830 6 + CB CT 0.06590 7 + HB1 HC 0.01020 8 + HB2 HC 0.01020 9 + CG CA -0.02050 10 + CD1 CA -0.20020 11 + HD1 HA 0.17200 12 + CE1 CA -0.22390 13 + HE1 HA 0.16500 14 + CZ C 0.31390 15 + OH OH -0.55780 16 + HH HO 0.40010 17 + CE2 CA -0.22390 18 + HE2 HA 0.16500 19 + CD2 CA -0.20020 20 + HD2 HA 0.17200 21 + C C 0.61230 22 + O O -0.57130 23 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG CD1 + CG CD2 + CD1 HD1 + CD1 CE1 + CE1 HE1 + CE1 CZ + CZ OH + CZ CE2 + OH HH + CE2 HE2 + CE2 CD2 + CD2 HD2 + C O + C +N + [ impropers ] + CA +N C O + CG CE2 CD2 HD2 + CZ CD2 CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + + +[ NGLU ] + [ atoms ] + N N3 0.00170 1 + H1 H 0.23910 2 + H2 H 0.23910 3 + H3 H 0.23910 4 + CA CX 0.05880 5 + HA HP 0.12020 6 + CB 2C 0.09090 7 + HB1 HC -0.02320 8 + HB2 HC -0.02320 9 + CG 2C -0.02360 10 + HG1 HC -0.03150 11 + HG2 HC -0.03150 12 + CD CO 0.80870 13 + OE1 O2 -0.81890 14 + OE2 O2 -0.81890 15 + C C 0.56210 16 + O O -0.58890 17 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD OE1 + CD OE2 + C O + C +N + [ impropers ] + CA +N C O + CG OE1 CD OE2 + +[ NASP ] + [ atoms ] + N N3 0.07820 1 + H1 H 0.22000 2 + H2 H 0.22000 3 + H3 H 0.22000 4 + CA CX 0.02920 5 + HA HP 0.11410 6 + CB 2C -0.02350 7 + HB1 HC -0.01690 8 + HB2 HC -0.01690 9 + CG CO 0.81940 10 + OD1 O2 -0.80840 11 + OD2 O2 -0.80840 12 + C C 0.56210 13 + O O -0.58890 14 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG OD1 + CG OD2 + C O + C +N + [ impropers ] + CA +N C O + CB OD1 CG OD2 + +[ NLYS ] + [ atoms ] + N N3 0.09660 1 + H1 H 0.21650 2 + H2 H 0.21650 3 + H3 H 0.21650 4 + CA CX -0.00150 5 + HA HP 0.11800 6 + CB C8 0.02120 7 + HB1 HC 0.02830 8 + HB2 HC 0.02830 9 + CG C8 -0.00480 10 + HG1 HC 0.01210 11 + HG2 HC 0.01210 12 + CD C8 -0.06080 13 + HD1 HC 0.06330 14 + HD2 HC 0.06330 15 + CE C8 -0.01810 16 + HE1 HP 0.11710 17 + HE2 HP 0.11710 18 + NZ N3 -0.37640 19 + HZ1 H 0.33820 20 + HZ2 H 0.33820 21 + HZ3 H 0.33820 22 + C C 0.72140 23 + O O -0.60130 24 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG CD + CD HD1 + CD HD2 + CD CE + CE HE1 + CE HE2 + CE NZ + NZ HZ1 + NZ HZ2 + NZ HZ3 + C O + C +N + [ impropers ] + CA +N C O + +[ NPRO ] + [ atoms ] + N N3 -0.20200 1 + H1 H 0.31200 2 + H2 H 0.31200 3 + CD CT -0.01200 4 + HD1 HP 0.10000 5 + HD2 HP 0.10000 6 + CG CT -0.12100 7 + HG1 HC 0.10000 8 + HG2 HC 0.10000 9 + CB CT -0.11500 10 + HB1 HC 0.10000 11 + HB2 HC 0.10000 12 + CA CX 0.10000 13 + HA HP 0.10000 14 + C C 0.52600 15 + O O -0.50000 16 + [ bonds ] + N H1 + N H2 + N CD + N CA + CD HD1 + CD HD2 + CD CG + CG HG1 + CG HG2 + CG CB + CB HB1 + CB HB2 + CB CA + CA HA + CA C + C O + C +N + [ impropers ] + CA +N C O + +[ NCYS ] + [ atoms ] + N N3 0.13250 1 + H1 H 0.20230 2 + H2 H 0.20230 3 + H3 H 0.20230 4 + CA CX 0.09270 5 + HA HP 0.14110 6 + CB 2C -0.11950 7 + HB1 H1 0.11880 8 + HB2 H1 0.11880 9 + SG SH -0.32980 10 + HG HS 0.19750 11 + C C 0.61230 12 + O O -0.57130 13 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB SG + SG HG + C O + C +N + [ impropers ] + CA +N C O + +[ NCYX ] + [ atoms ] + N N3 0.20690 1 + H1 H 0.18150 2 + H2 H 0.18150 3 + H3 H 0.18150 4 + CA CX 0.10550 5 + HA HP 0.09220 6 + CB 2C -0.02770 7 + HB1 H1 0.06800 8 + HB2 H1 0.06800 9 + SG S -0.09840 10 + C C 0.61230 11 + O O -0.57130 12 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB2 + CB HB1 + CB SG + C O + C +N + [ impropers ] + CA +N C O + +[ NMET ] + [ atoms ] + N N3 0.15920 1 + H1 H 0.19840 2 + H2 H 0.19840 3 + H3 H 0.19840 4 + CA CX 0.02210 5 + HA HP 0.11160 6 + CB 2C 0.08650 7 + HB1 HC 0.01250 8 + HB2 HC 0.01250 9 + CG 2C 0.03340 10 + HG1 H1 0.02920 11 + HG2 H1 0.02920 12 + SD S -0.27740 13 + CE CT -0.03410 14 + HE1 H1 0.05970 15 + HE2 H1 0.05970 16 + HE3 H1 0.05970 17 + C C 0.61230 18 + O O -0.57130 19 + [ bonds ] + N H1 + N H2 + N H3 + N CA + CA HA + CA CB + CA C + CB HB1 + CB HB2 + CB CG + CG HG1 + CG HG2 + CG SD + SD CE + CE HE1 + CE HE2 + CE HE3 + C O + C +N + [ impropers ] + CA +N C O + diff --git a/tests/test_files/assets/amber14sb.ff/aminoacids.vsd b/tests/test_files/assets/amber14sb.ff/aminoacids.vsd new file mode 100644 index 0000000..fa52c67 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/aminoacids.vsd @@ -0,0 +1,225 @@ + +[ CH3 ] +; CT sp3 aliphatic C + ;bound to sp2/sp3 carbons + CT C MCH3 + CT CA MCH3 + CT CB MCH3 + CT CC MCH3 + CT CK MCH3 + CT CM MCH3 + CT CN MCH3 + CT CQ MCH3 + CT CR MCH3 + CT CT MCH3 + CT CV MCH3 + CT CW MCH3 + CT C* MCH3 + CT N MCH3 + CT S MCH3 + +[ NH3 ] +; N3 sp3 N for charged amino groups + N3 C MNH3 + N3 CA MNH3 + N3 CB MNH3 + N3 CC MNH3 + N3 CK MNH3 + N3 CM MNH3 + N3 CN MNH3 + N3 CQ MNH3 + N3 CR MNH3 + N3 CT MNH3 + N3 CV MNH3 + N3 CW MNH3 + N3 C* MNH3 + +[ NH2 ] +; N sp2 nitrogen in amide groups + N planar + N2 planar + + +; Data for generating dummy aromatic rings. +; Actually we dont need all these bonds and angles, +; but by specifying them here it is easier to improve +; the dummy generation code later. +[ PHE ] + CG CD1 0.140 + CG CD2 0.140 + CD1 CE1 0.140 + CD2 CE2 0.140 + CE1 CZ 0.140 + CE2 CZ 0.140 + CD1 HD1 0.108 + CD2 HD2 0.108 + CE1 HE1 0.108 + CE2 HE2 0.108 + CZ HZ 0.108 + CG CD1 CE1 120.0 + CD1 CE1 CZ 120.0 + CE1 CZ CE2 120.0 + CZ CE2 CD2 120.0 + CE2 CD2 CG 120.0 + CD2 CG CD1 120.0 + CG CD1 HD1 120.0 + CG CD2 HD2 120.0 + HD1 CD1 CE1 120.0 + CD1 CE1 HE1 120.0 + HE1 CE1 CZ 120.0 + CE1 CZ HZ 120.0 + HZ CZ CE2 120.0 + CZ CE2 HE2 120.0 + HE2 CE2 CD2 120.0 + HD2 CD2 CG 120.0 + + +[ TYR ] + CG CD1 0.140 + CG CD2 0.140 + CD1 CE1 0.140 + CD2 CE2 0.140 + CE1 CZ 0.140 + CE2 CZ 0.140 + CD1 HD1 0.108 + CD2 HD2 0.108 + CE1 HE1 0.108 + CE2 HE2 0.108 + CZ OH 0.1364 + OH HH 0.0945 + CG CD1 CE1 120.0 + CD1 CE1 CZ 120.0 + CE1 CZ CE2 120.0 + CZ CE2 CD2 120.0 + CE2 CD2 CG 120.0 + CD2 CG CD1 120.0 + CG CD1 HD1 120.0 + CG CD2 HD2 120.0 + HD1 CD1 CE1 120.0 + CD1 CE1 HE1 120.0 + HE1 CE1 CZ 120.0 + CE1 CZ OH 120.0 + CZ OH HH 113.0 + OH CZ CE2 120.0 + CZ CE2 HE2 120.0 + HE2 CE2 CD2 120.0 + HD2 CD2 CG 120.0 + + +[ TRP ] ; angles from MD sim, corrected to be perfectly planar + CB CG 0.1495 + CG CD1 0.1352 + CD1 NE1 0.1381 + NE1 CE2 0.138 + CE2 CD2 0.1419 + CD2 CG 0.1459 + CE2 CZ2 0.140 + CZ2 CH2 0.140 + CH2 CZ3 0.140 + CZ3 CE3 0.140 + CE3 CD2 0.1404 + CD1 HD1 0.108 + NE1 HE1 0.101 + CE3 HE3 0.108 + CZ2 HZ2 0.108 + CZ3 HZ3 0.108 + CH2 HH2 0.108 + CB CG CD1 125.6 + CB CG CD2 128.7 + CG CD1 NE1 109.7 + CD1 NE1 CE2 111.7 + NE1 CE2 CD2 104.3 + CE2 CD2 CG 108.5 + CD2 CG CD1 105.7 + NE1 CE2 CZ2 135.7 + CE2 CZ2 CH2 120.0 + CZ2 CH2 CZ3 120.0 + CH2 CZ3 CE3 120.0 + CZ3 CE3 CD2 120.0 + CE2 CD2 CE3 120.0 + CD2 CE2 CZ2 120.0 + CE3 CD2 CG 131.5 + CG CD1 HD1 124.6 + HD1 CD1 NE1 125.7 + CD1 NE1 HE1 122.7 + HE1 NE1 CE2 125.6 + CZ3 CE3 HE3 120.0 + HE3 CE3 CD2 120.0 + CE2 CZ2 HZ2 120.0 + HZ2 CZ2 CH2 120.0 + CH2 CZ3 HZ3 120.0 + HZ3 CZ3 CE3 120.0 + CZ2 CH2 HH2 120.0 + HH2 CH2 CZ3 120.0 + + +[ HID ] ; angles from MD sim, corrected to be perfectly planar + CG ND1 0.1381 + ND1 CE1 0.1343 + CE1 NE2 0.1335 + NE2 CD2 0.1394 + CD2 CG 0.137 + ND1 HD1 0.101 + CE1 HE1 0.108 + CD2 HD2 0.108 + CG ND1 CE1 107.4 + ND1 CE1 NE2 113.1 + CE1 NE2 CD2 104.5 + NE2 CD2 CG 109.3 + CD2 CG ND1 105.7 + CG ND1 HD1 127.7 + HD1 ND1 CE1 124.9 + ND1 CE1 HE1 122.9 + HE1 CE1 NE2 124.0 + CG CD2 HD2 129.0 + HD2 CD2 NE2 121.7 + + +[ HIE ] ; angles from MD sim, corrected to be perfectly planar + CG ND1 0.1394 + ND1 CE1 0.1335 + CE1 NE2 0.1343 + NE2 CD2 0.1381 + CD2 CG 0.137 + CD2 HD2 0.108 + CE1 HE1 0.108 + NE2 HE2 0.101 + CG ND1 CE1 104.9 + ND1 CE1 NE2 112.9 + CE1 NE2 CD2 107.3 + NE2 CD2 CG 106.4 + CD2 CG ND1 108.5 + NE2 CD2 HD2 122.4 + HD2 CD2 CG 131.2 + ND1 CE1 HE1 123.8 + HE1 CE1 NE2 123.3 + CE1 NE2 HE2 125.9 + HE2 NE2 CD2 126.8 + + +[ HIP ] ; angles from MD sim, corrected to be perfectly planar + CG ND1 0.1381 + ND1 CE1 0.1343 + CE1 NE2 0.1343 + NE2 CD2 0.1381 + CD2 CG 0.137 + ND1 HD1 0.101 + CE1 HE1 0.108 + CD2 HD2 0.108 + NE2 HE2 0.101 + CG ND1 CE1 107.4 + ND1 CE1 NE2 111.4 + CE1 NE2 CD2 107.2 + NE2 CD2 CG 107.4 + CD2 CG ND1 106.6 + CG ND1 HD1 127.4 + HD1 ND1 CE1 125.2 + ND1 CE1 HE1 124.3 + HE1 CE1 NE2 124.3 + CE1 NE2 HE2 126.4 + HE2 NE2 CD2 126.4 + NE2 CD2 HD2 120.8 + HD2 CD2 CG 131.8 + + + diff --git a/tests/test_files/assets/amber14sb.ff/atomtypes.atp b/tests/test_files/assets/amber14sb.ff/atomtypes.atp new file mode 100644 index 0000000..8847740 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/atomtypes.atp @@ -0,0 +1,84 @@ +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CD 12.01000 ; +CI 12.01000 ; +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CO 12.01000 ; +CP 12.01000 ; +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CS 12.01000 ; +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +CX 12.01000 ; +CY 12.01000 ; +CZ 12.01000 ; +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +2C 12.01000 ; +3C 12.01000 ; +C4 12.01000 ; +C5 12.01000 ; +C8 12.01000 ; +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +HZ 1.00800 ; +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +NT 14.01000 ; +NY 14.01000 ; +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +OP 16.00000 ; +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +EP 0.00000 ; diff --git a/tests/test_files/assets/amber14sb.ff/dna.arn b/tests/test_files/assets/amber14sb.ff/dna.arn new file mode 100644 index 0000000..ef4db90 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/dna.arn @@ -0,0 +1,8 @@ +DNA OP1 O1P +DNA OP2 O2P +DNA H2' H2'1 +DNA H2'' H2'2 +DNA H5' H5'1 +DNA H5'' H5'2 +DNA HO5' H5T +DNA HO3' H3T diff --git a/tests/test_files/assets/amber14sb.ff/dna.hdb b/tests/test_files/assets/amber14sb.ff/dna.hdb new file mode 100644 index 0000000..09f83f7 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/dna.hdb @@ -0,0 +1,160 @@ +DA5 9 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DA 8 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DA3 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DAN 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DT5 9 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DT 8 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DT3 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DTN 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DG5 9 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DG 8 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DG3 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DGN 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DC5 9 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DC 8 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DC3 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +DCN 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' diff --git a/tests/test_files/assets/amber14sb.ff/dna.r2b b/tests/test_files/assets/amber14sb.ff/dna.r2b new file mode 100644 index 0000000..285ec3b --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/dna.r2b @@ -0,0 +1,6 @@ +; rtp residue to rtp building block table +;GMX Force-field +DA DA DA5 DA3 DAN +DG DG DG5 DG3 DGN +DC DC DC5 DC3 DCN +DT DT DT5 DT3 DTN diff --git a/tests/test_files/assets/amber14sb.ff/dna.rtp b/tests/test_files/assets/amber14sb.ff/dna.rtp new file mode 100644 index 0000000..1170a78 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/dna.rtp @@ -0,0 +1,1223 @@ +[ bondedtypes ] +; Col 1: Type of bond +; Col 2: Type of angles +; Col 3: Type of proper dihedrals +; Col 4: Type of improper dihedrals +; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. +; Col 6: Number of excluded neighbors for nonbonded interactions +; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 +; Col 8: Remove impropers over the same bond as a proper if it is 1 +; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih + 1 1 9 4 1 3 1 0 + + +; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's + +[ DA5 ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT 0.04310 9 + H1' H2 0.18380 10 + N9 N* -0.02680 11 + C8 CK 0.16070 12 + H8 H5 0.18770 13 + N7 NB -0.61750 14 + C5 CB 0.07250 15 + C6 CA 0.68970 16 + N6 N2 -0.91230 17 + H61 H 0.41670 18 + H62 H 0.41670 19 + N1 NC -0.76240 20 + C2 CQ 0.57160 21 + H2 H5 0.05980 22 + N3 NC -0.74170 23 + C4 CB 0.38000 24 + C3' CT 0.07130 25 + H3' H1 0.09850 26 + C2' CT -0.08540 27 + H2'1 HC 0.07180 28 + H2'2 HC 0.07180 29 + O3' OS -0.52320 30 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + +[ DA ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT 0.04310 11 + H1' H2 0.18380 12 + N9 N* -0.02680 13 + C8 CK 0.16070 14 + H8 H5 0.18770 15 + N7 NB -0.61750 16 + C5 CB 0.07250 17 + C6 CA 0.68970 18 + N6 N2 -0.91230 19 + H61 H 0.41670 20 + H62 H 0.41670 21 + N1 NC -0.76240 22 + C2 CQ 0.57160 23 + H2 H5 0.05980 24 + N3 NC -0.74170 25 + C4 CB 0.38000 26 + C3' CT 0.07130 27 + H3' H1 0.09850 28 + C2' CT -0.08540 29 + H2'1 HC 0.07180 30 + H2'2 HC 0.07180 31 + O3' OS -0.52320 32 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + -O3' P + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + +[ DA3 ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT 0.04310 11 + H1' H2 0.18380 12 + N9 N* -0.02680 13 + C8 CK 0.16070 14 + H8 H5 0.18770 15 + N7 NB -0.61750 16 + C5 CB 0.07250 17 + C6 CA 0.68970 18 + N6 N2 -0.91230 19 + H61 H 0.41670 20 + H62 H 0.41670 21 + N1 NC -0.76240 22 + C2 CQ 0.57160 23 + H2 H5 0.05980 24 + N3 NC -0.74170 25 + C4 CB 0.38000 26 + C3' CT 0.07130 27 + H3' H1 0.09850 28 + C2' CT -0.08540 29 + H2'1 HC 0.07180 30 + H2'2 HC 0.07180 31 + O3' OH -0.65490 32 + H3T HO 0.43960 33 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + -O3' P + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + +[ DAN ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT 0.04310 9 + H1' H2 0.18380 10 + N9 N* -0.02680 11 + C8 CK 0.16070 12 + H8 H5 0.18770 13 + N7 NB -0.61750 14 + C5 CB 0.07250 15 + C6 CA 0.68970 16 + N6 N2 -0.91230 17 + H61 H 0.41670 18 + H62 H 0.41670 19 + N1 NC -0.76240 20 + C2 CQ 0.57160 21 + H2 H5 0.05980 22 + N3 NC -0.74170 23 + C4 CB 0.38000 24 + C3' CT 0.07130 25 + H3' H1 0.09850 26 + C2' CT -0.08540 27 + H2'1 HC 0.07180 28 + H2'2 HC 0.07180 29 + O3' OH -0.65490 30 + H3T HO 0.43960 31 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + + + +[ DT5 ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT 0.06800 9 + H1' H2 0.18040 10 + N1 N* -0.02390 11 + C6 CM -0.22090 12 + H6 H4 0.26070 13 + C5 CM 0.00250 14 + C7 CT -0.22690 15 + H71 HC 0.07700 16 + H72 HC 0.07700 17 + H73 HC 0.07700 18 + C4 C 0.51940 19 + O4 O -0.55630 20 + N3 NA -0.43400 21 + H3 H 0.34200 22 + C2 C 0.56770 23 + O2 O -0.58810 24 + C3' CT 0.07130 25 + H3' H1 0.09850 26 + C2' CT -0.08540 27 + H2'1 HC 0.07180 28 + H2'2 HC 0.07180 29 + O3' OS -0.52320 30 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 C7 + C5 C4 + C7 H71 + C7 H72 + C7 H73 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + [ impropers ] + C2 C6 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + +[ DT ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT 0.06800 11 + H1' H2 0.18040 12 + N1 N* -0.02390 13 + C6 CM -0.22090 14 + H6 H4 0.26070 15 + C5 CM 0.00250 16 + C7 CT -0.22690 17 + H71 HC 0.07700 18 + H72 HC 0.07700 19 + H73 HC 0.07700 20 + C4 C 0.51940 21 + O4 O -0.55630 22 + N3 NA -0.43400 23 + H3 H 0.34200 24 + C2 C 0.56770 25 + O2 O -0.58810 26 + C3' CT 0.07130 27 + H3' H1 0.09850 28 + C2' CT -0.08540 29 + H2'1 HC 0.07180 30 + H2'2 HC 0.07180 31 + O3' OS -0.52320 32 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 C7 + C5 C4 + C7 H71 + C7 H72 + C7 H73 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + -O3' P + [ impropers ] + C2 C6 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + +[ DT3 ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT 0.06800 11 + H1' H2 0.18040 12 + N1 N* -0.02390 13 + C6 CM -0.22090 14 + H6 H4 0.26070 15 + C5 CM 0.00250 16 + C7 CT -0.22690 17 + H71 HC 0.07700 18 + H72 HC 0.07700 19 + H73 HC 0.07700 20 + C4 C 0.51940 21 + O4 O -0.55630 22 + N3 NA -0.43400 23 + H3 H 0.34200 24 + C2 C 0.56770 25 + O2 O -0.58810 26 + C3' CT 0.07130 27 + H3' H1 0.09850 28 + C2' CT -0.08540 29 + H2'1 HC 0.07180 30 + H2'2 HC 0.07180 31 + O3' OH -0.65490 32 + H3T HO 0.43960 33 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 C7 + C5 C4 + C7 H71 + C7 H72 + C7 H73 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + -O3' P + [ impropers ] + C2 C6 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + +[ DTN ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT 0.06800 9 + H1' H2 0.18040 10 + N1 N* -0.02390 11 + C6 CM -0.22090 12 + H6 H4 0.26070 13 + C5 CM 0.00250 14 + C7 CT -0.22690 15 + H71 HC 0.07700 16 + H72 HC 0.07700 17 + H73 HC 0.07700 18 + C4 C 0.51940 19 + O4 O -0.55630 20 + N3 NA -0.43400 21 + H3 H 0.34200 22 + C2 C 0.56770 23 + O2 O -0.58810 24 + C3' CT 0.07130 25 + H3' H1 0.09850 26 + C2' CT -0.08540 27 + H2'1 HC 0.07180 28 + H2'2 HC 0.07180 29 + O3' OH -0.65490 30 + H3T HO 0.43960 31 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 C7 + C5 C4 + C7 H71 + C7 H72 + C7 H73 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + [ impropers ] + C2 C6 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + + + +[ DG5 ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT 0.03580 9 + H1' H2 0.17460 10 + N9 N* 0.05770 11 + C8 CK 0.07360 12 + H8 H5 0.19970 13 + N7 NB -0.57250 14 + C5 CB 0.19910 15 + C6 C 0.49180 16 + O6 O -0.56990 17 + N1 NA -0.50530 18 + H1 H 0.35200 19 + C2 CA 0.74320 20 + N2 N2 -0.92300 21 + H21 H 0.42350 22 + H22 H 0.42350 23 + N3 NC -0.66360 24 + C4 CB 0.18140 25 + C3' CT 0.07130 26 + H3' H1 0.09850 27 + C2' CT -0.08540 28 + H2'1 HC 0.07180 29 + H2'2 HC 0.07180 30 + O3' OS -0.52320 31 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ DG ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT 0.03580 11 + H1' H2 0.17460 12 + N9 N* 0.05770 13 + C8 CK 0.07360 14 + H8 H5 0.19970 15 + N7 NB -0.57250 16 + C5 CB 0.19910 17 + C6 C 0.49180 18 + O6 O -0.56990 19 + N1 NA -0.50530 20 + H1 H 0.35200 21 + C2 CA 0.74320 22 + N2 N2 -0.92300 23 + H21 H 0.42350 24 + H22 H 0.42350 25 + N3 NC -0.66360 26 + C4 CB 0.18140 27 + C3' CT 0.07130 28 + H3' H1 0.09850 29 + C2' CT -0.08540 30 + H2'1 HC 0.07180 31 + H2'2 HC 0.07180 32 + O3' OS -0.52320 33 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + -O3' P + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ DG3 ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT 0.03580 11 + H1' H2 0.17460 12 + N9 N* 0.05770 13 + C8 CK 0.07360 14 + H8 H5 0.19970 15 + N7 NB -0.57250 16 + C5 CB 0.19910 17 + C6 C 0.49180 18 + O6 O -0.56990 19 + N1 NA -0.50530 20 + H1 H 0.35200 21 + C2 CA 0.74320 22 + N2 N2 -0.92300 23 + H21 H 0.42350 24 + H22 H 0.42350 25 + N3 NC -0.66360 26 + C4 CB 0.18140 27 + C3' CT 0.07130 28 + H3' H1 0.09850 29 + C2' CT -0.08540 30 + H2'1 HC 0.07180 31 + H2'2 HC 0.07180 32 + O3' OH -0.65490 33 + H3T HO 0.43960 34 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + -O3' P + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ DGN ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT 0.03580 9 + H1' H2 0.17460 10 + N9 N* 0.05770 11 + C8 CK 0.07360 12 + H8 H5 0.19970 13 + N7 NB -0.57250 14 + C5 CB 0.19910 15 + C6 C 0.49180 16 + O6 O -0.56990 17 + N1 NA -0.50530 18 + H1 H 0.35200 19 + C2 CA 0.74320 20 + N2 N2 -0.92300 21 + H21 H 0.42350 22 + H22 H 0.42350 23 + N3 NC -0.66360 24 + C4 CB 0.18140 25 + C3' CT 0.07130 26 + H3' H1 0.09850 27 + C2' CT -0.08540 28 + H2'1 HC 0.07180 29 + H2'2 HC 0.07180 30 + O3' OH -0.65490 31 + H3T HO 0.43960 32 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ DC5 ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT -0.01160 9 + H1' H2 0.19630 10 + N1 N* -0.03390 11 + C6 CM -0.01830 12 + H6 H4 0.22930 13 + C5 CM -0.52220 14 + H5 HA 0.18630 15 + C4 CA 0.84390 16 + N4 N2 -0.97730 17 + H41 H 0.43140 18 + H42 H 0.43140 19 + N3 NC -0.77480 20 + C2 C 0.79590 21 + O2 O -0.65480 22 + C3' CT 0.07130 23 + H3' H1 0.09850 24 + C2' CT -0.08540 25 + H2'1 HC 0.07180 26 + H2'2 HC 0.07180 27 + O3' OS -0.52320 28 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + [ impropers ] + C1' N1 C6 C2 + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + +[ DC ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT -0.01160 11 + H1' H2 0.19630 12 + N1 N* -0.03390 13 + C6 CM -0.01830 14 + H6 H4 0.22930 15 + C5 CM -0.52220 16 + H5 HA 0.18630 17 + C4 CA 0.84390 18 + N4 N2 -0.97730 19 + H41 H 0.43140 20 + H42 H 0.43140 21 + N3 NC -0.77480 22 + C2 C 0.79590 23 + O2 O -0.65480 24 + C3' CT 0.07130 25 + H3' H1 0.09850 26 + C2' CT -0.08540 27 + H2'1 HC 0.07180 28 + H2'2 HC 0.07180 29 + O3' OS -0.52320 30 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + -O3' P + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + +[ DC3 ] + [ atoms ] + P P 1.16590 1 + O1P O2 -0.77610 2 + O2P O2 -0.77610 3 + O5' OS -0.49540 4 + C5' CI -0.00690 5 + H5'1 H1 0.07540 6 + H5'2 H1 0.07540 7 + C4' CT 0.16290 8 + H4' H1 0.11760 9 + O4' OS -0.36910 10 + C1' CT -0.01160 11 + H1' H2 0.19630 12 + N1 N* -0.03390 13 + C6 CM -0.01830 14 + H6 H4 0.22930 15 + C5 CM -0.52220 16 + H5 HA 0.18630 17 + C4 CA 0.84390 18 + N4 N2 -0.97730 19 + H41 H 0.43140 20 + H42 H 0.43140 21 + N3 NC -0.77480 22 + C2 C 0.79590 23 + O2 O -0.65480 24 + C3' CT 0.07130 25 + H3' H1 0.09850 26 + C2' CT -0.08540 27 + H2'1 HC 0.07180 28 + H2'2 HC 0.07180 29 + O3' OH -0.65490 30 + H3T HO 0.43960 31 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + -O3' P + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + +[ DCN ] + [ atoms ] + H5T HO 0.44220 1 + O5' OH -0.63180 2 + C5' CI -0.00690 3 + H5'1 H1 0.07540 4 + H5'2 H1 0.07540 5 + C4' CT 0.16290 6 + H4' H1 0.11760 7 + O4' OS -0.36910 8 + C1' CT -0.01160 9 + H1' H2 0.19630 10 + N1 N* -0.03390 11 + C6 CM -0.01830 12 + H6 H4 0.22930 13 + C5 CM -0.52220 14 + H5 HA 0.18630 15 + C4 CA 0.84390 16 + N4 N2 -0.97730 17 + H41 H 0.43140 18 + H42 H 0.43140 19 + N3 NC -0.77480 20 + C2 C 0.79590 21 + O2 O -0.65480 22 + C3' CT 0.07130 23 + H3' H1 0.09850 24 + C2' CT -0.08540 25 + H2'1 HC 0.07180 26 + H2'2 HC 0.07180 27 + O3' OH -0.65490 28 + H3T HO 0.43960 29 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' H2'2 + O3' H3T + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C4 N4 C5 + diff --git a/tests/test_files/assets/amber14sb.ff/ffbonded.itp b/tests/test_files/assets/amber14sb.ff/ffbonded.itp new file mode 100644 index 0000000..6745f7e --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/ffbonded.itp @@ -0,0 +1,1401 @@ +[ bondtypes ] +; i j func b0 kb + C C 1 0.15250 259408.0 + C CA 1 0.14090 392459.2 + C CB 1 0.14190 374049.6 + C CM 1 0.14440 343088.0 + C CS 1 0.14440 343088.0 + C CT 1 0.15220 265265.6 + C CX 1 0.15220 265265.6 + C N 1 0.13350 410032.0 + C N* 1 0.13830 354803.2 + C NA 1 0.13880 349782.4 + C NC 1 0.13580 382417.6 + C O 1 0.12290 476976.0 + C O2 1 0.12500 548940.8 + C OH 1 0.13640 376560.0 + C OS 1 0.13230 376560.0 + C H4 1 0.10800 307105.6 + C H5 1 0.10800 307105.6 + CA CA 1 0.14000 392459.2 + CA CB 1 0.14040 392459.2 + CA CM 1 0.14330 357313.6 + CA CS 1 0.14330 357313.6 + CA CN 1 0.14000 392459.2 + CA CT 1 0.15100 265265.6 + CA HA 1 0.10800 307105.6 + CA H4 1 0.10800 307105.6 + CA N2 1 0.13400 402500.8 + CA NA 1 0.13810 357313.6 + CA NC 1 0.13390 404174.4 + CA OH 1 0.13640 376560.0 + CB CB 1 0.13700 435136.0 + CB N* 1 0.13740 364844.8 + CB NB 1 0.13910 346435.2 + CB NC 1 0.13540 385764.8 + CD HA 1 0.10800 307105.6 + CD CD 1 0.14000 392459.2 + CD CM 1 0.13500 459403.2 + CD CS 1 0.13500 459403.2 + CD CT 1 0.15100 265265.6 + CK H5 1 0.10800 307105.6 + CK N* 1 0.13710 368192.0 + CK NB 1 0.13040 442667.2 + CP H5 1 0.10800 307105.6 + CP N* 1 0.13710 368192.0 + CP NB 1 0.13040 442667.2 + CM CM 1 0.13500 459403.2 + CM CT 1 0.15100 265265.6 + CM HA 1 0.10800 307105.6 + CM H4 1 0.10800 307105.6 + CM H5 1 0.10800 307105.6 + CM N* 1 0.13650 374886.4 + CM OS 1 0.12400 401664.0 + CS CS 1 0.13500 459403.2 + CS CT 1 0.15100 265265.6 + CS HA 1 0.10800 307105.6 + CS H4 1 0.10800 307105.6 + CS H5 1 0.10800 307105.6 + CS N* 1 0.13650 374886.4 + CS OS 1 0.12400 401664.0 + CQ H5 1 0.10800 307105.6 + CQ NC 1 0.13240 420073.6 + CT CT 1 0.15260 259408.0 + CX CT 1 0.15260 259408.0 + CT HC 1 0.10900 284512.0 + CT H1 1 0.10900 284512.0 + CX H1 1 0.10900 284512.0 + CT H2 1 0.10900 284512.0 + CT H3 1 0.10900 284512.0 + CT HP 1 0.10900 284512.0 + CX HP 1 0.10900 284512.0 + CT N* 1 0.14750 282001.6 + CT N2 1 0.14630 282001.6 + CT OH 1 0.14100 267776.0 + CT OS 1 0.14100 267776.0 + C* HC 1 0.10800 307105.6 + C* CB 1 0.14590 324678.4 + C* CT 1 0.14950 265265.6 + C* CW 1 0.13520 456892.8 + CB CN 1 0.14190 374049.6 + CC CT 1 0.15040 265265.6 + CC CV 1 0.13750 428441.6 + CC CW 1 0.13710 433462.4 + CC NA 1 0.13850 353129.6 + CC NB 1 0.13940 343088.0 + CN NA 1 0.13800 358150.4 + CR H5 1 0.10800 307105.6 + CR NA 1 0.13430 399153.6 + CR NB 1 0.13350 408358.4 + CT N 1 0.14490 282001.6 + CX N 1 0.14490 282001.6 + CT N3 1 0.14710 307105.6 + CX N3 1 0.14710 307105.6 + CT NT 1 0.14710 307105.6 + CT S 1 0.18100 189953.6 + CT SH 1 0.18100 198321.6 + CT CY 1 0.14580 334720.0 + CT CZ 1 0.14590 334720.0 + CV H4 1 0.10800 307105.6 + CV NB 1 0.13940 343088.0 + CW H4 1 0.10800 307105.6 + CW NA 1 0.13810 357313.6 + CY NY 1 0.11500 502080.0 + CZ CZ 1 0.12060 502080.0 + CZ HZ 1 0.10560 334720.0 + OP P 1 0.14800 439320.0 + O2 P 1 0.14800 439320.0 + OH P 1 0.16100 192464.0 + OS P 1 0.16100 192464.0 + NA P 1 0.18400 209200.0 + H N2 1 0.10100 363171.2 + H N* 1 0.10100 363171.2 + H NA 1 0.10100 363171.2 + H N 1 0.10100 363171.2 + H N3 1 0.10100 363171.2 + H NT 1 0.10100 363171.2 + HO OH 1 0.09600 462750.4 + HO OS 1 0.09600 462750.4 + HS SH 1 0.13360 229283.2 + S S 1 0.20380 138908.8 + F CT 1 0.13800 307105.6 + Cl CT 1 0.17660 194137.6 + Br CT 1 0.19440 133051.2 + I CT 1 0.21660 123846.4 + F CA 1 0.13590 323004.8 + Cl CA 1 0.17270 161502.4 + I CA 1 0.20750 143092.8 + Br CA 1 0.18900 143929.6 + EP O 1 0.02000 502080.0 + EP OH 1 0.02000 502080.0 + EP OS 1 0.02000 502080.0 + EP N3 1 0.02000 502080.0 + EP NT 1 0.02000 502080.0 + EP NB 1 0.02000 502080.0 + EP NC 1 0.02000 502080.0 + EP S 1 0.07000 502080.0 + EP SH 1 0.07000 502080.0 + CI H1 1 0.10900 284512.0 + CI CT 1 0.15260 259408.0 + OS CI 1 0.14100 267776.0 + OH CI 1 0.14100 267776.0 + C5 H5 1 0.10800 307105.6 + C5 N* 1 0.13710 368192.0 + C5 NB 1 0.13040 442667.2 + C C4 1 0.14440 343088.0 + CA C4 1 0.14330 357313.6 + C4 C4 1 0.13500 459403.2 + C4 CT 1 0.15100 265265.6 + C4 HA 1 0.10800 307105.6 + C4 H4 1 0.10800 307105.6 + C4 N* 1 0.13650 374886.4 + C 2C 1 0.15220 265265.6 + C* 2C 1 0.14950 265265.6 + C8 C8 1 0.15260 259408.0 + C8 CX 1 0.15260 259408.0 + C8 H1 1 0.10900 284512.0 + C8 HC 1 0.10900 284512.0 + C8 HP 1 0.10900 284512.0 + C8 N2 1 0.14630 282001.6 + C8 N3 1 0.14710 307105.6 + CA 2C 1 0.15100 265265.6 + CC 2C 1 0.15040 265265.6 + CO O2 1 0.12500 548940.8 + CO 2C 1 0.15220 265265.6 + CT 2C 1 0.15260 259408.0 + CT 3C 1 0.15260 259408.0 + CX 2C 1 0.15260 259408.0 + CX 3C 1 0.15260 259408.0 + H1 2C 1 0.10900 284512.0 + H1 3C 1 0.10900 284512.0 + HC 2C 1 0.10900 284512.0 + HC 3C 1 0.10900 284512.0 + OH 2C 1 0.14100 267776.0 + OH 3C 1 0.14100 267776.0 + S 2C 1 0.18100 189953.6 + SH 2C 1 0.18100 198321.6 + 2C 2C 1 0.15260 259408.0 + 2C 3C 1 0.15260 259408.0 + + + +[ constrainttypes ] +; this section is implemented manually from bond & angle values + +; constraints for rigid CH3 groups + MCH3 CT 2 0.166426 + MCH3 S 2 0.193875 + MCH3 MCH3 2 0.092163 +; constraints for rigid NH3 groups + MNH3 CT 2 0.158254 + MNH3 MNH3 2 0.080229 + +; angle-derived constraints for OH and SH groups in proteins +; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C. + C HO 2 0.195074 + CA HO 2 0.195074 + CT HO 2 0.194132 + CT HS 2 0.235935 + + +[ angletypes ] +; i j k func th0 cth +HW OW HW 1 104.520 836.800 ; TIP3P water +HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds) +C C O 1 120.000 669.440 +C C OH 1 120.000 669.440 +CA C CA 1 120.000 527.184 +CA C OH 1 120.000 585.760 +CA C OS 1 120.000 585.760 +CC NA P 1 125.100 641.826 +CR NA P 1 125.100 641.826 +NA P OP 1 102.380 358.987 +CB C NA 1 111.300 585.760 +CB C O 1 128.800 669.440 +CM C NA 1 114.100 585.760 +CM C O 1 125.300 669.440 +CS C NA 1 114.100 585.760 +CS C O 1 125.300 669.440 +CT C O 1 120.400 669.440 +CX C O 1 120.400 669.440 +CT C O2 1 117.000 585.760 +CX C O2 1 117.000 585.760 +CT C N 1 116.600 585.760 +CX C N 1 116.600 585.760 +CT C CT 1 117.000 527.184 +CT C OS 1 115.000 669.440 +CT C OH 1 110.000 669.440 +CX C OH 1 110.000 669.440 +N* C NA 1 115.400 585.760 +N* C NC 1 118.600 585.760 +N* C O 1 120.900 669.440 +NA C O 1 120.600 669.440 +NC C O 1 122.500 669.440 +N C O 1 122.900 669.440 +O C O 1 126.000 669.440 +O C OH 1 120.000 669.440 +O C OS 1 125.000 669.440 +O2 C O2 1 126.000 669.440 +H4 C C 1 120.000 418.400 +H4 C CM 1 115.000 418.400 +H4 C CS 1 115.000 418.400 +H4 C CT 1 115.000 418.400 +H4 C O 1 120.000 418.400 +H4 C OH 1 120.000 418.400 +H5 C N 1 120.000 418.400 +H5 C O 1 119.000 418.400 +H5 C OH 1 107.000 418.400 +H5 C OS 1 107.000 418.400 +C CA CA 1 120.000 527.184 +C CA HA 1 120.000 418.400 +CA CA CA 1 120.000 527.184 +CA CA CB 1 120.000 527.184 +CA CA CT 1 120.000 585.760 +CA CA HA 1 120.000 418.400 +CA CA H4 1 120.000 418.400 +CA CA OH 1 120.000 585.760 +CA CA CN 1 120.000 527.184 +CB CA HA 1 120.000 418.400 +CB CA H4 1 120.000 418.400 +CB CA N2 1 123.500 585.760 +CB CA NC 1 117.300 585.760 +CM CA N2 1 120.100 585.760 +CM CA NC 1 121.500 585.760 +CS CA N2 1 120.100 585.760 +CS CA NC 1 121.500 585.760 +CN CA HA 1 120.000 418.400 +NA CA NC 1 123.300 585.760 +N2 CA NA 1 116.000 585.760 +N2 CA NC 1 119.300 585.760 +N2 CA N2 1 120.000 585.760 +F CA CA 1 121.000 585.760 +Cl CA CA 1 118.800 585.760 +Br CA CA 1 118.800 585.760 +I CA CA 1 118.800 585.760 +C CB CB 1 119.200 527.184 +C CB NB 1 130.000 585.760 +CA CB CB 1 117.300 527.184 +CA CB NB 1 132.400 585.760 +CB CB N* 1 106.200 585.760 +CB CB NB 1 110.400 585.760 +CB CB NC 1 127.700 585.760 +C* CB CA 1 134.900 527.184 +C* CB CN 1 108.800 527.184 +CA CB CN 1 116.200 527.184 +N* CB NC 1 126.200 585.760 +CD CD CM 1 120.000 527.184 +CD CD CS 1 120.000 527.184 +CD CD CT 1 120.000 585.760 +CM CD CT 1 120.000 585.760 +CS CD CT 1 120.000 585.760 +HA CD HA 1 119.000 292.880 +HA CD CD 1 120.000 418.400 +HA CD CM 1 120.000 418.400 +HA CD CS 1 120.000 418.400 +H5 CK N* 1 123.050 418.400 +H5 CK NB 1 123.050 418.400 +N* CK NB 1 113.900 585.760 +H5 CP N* 1 123.050 418.400 +H5 CP NB 1 123.050 418.400 +N* CP NB 1 113.900 585.760 +C CM CM 1 120.700 527.184 +C CM CT 1 119.700 585.760 +C CM HA 1 119.700 418.400 +C CM H4 1 119.700 418.400 +CA CM CM 1 117.000 527.184 +CA CM HA 1 123.300 418.400 +CA CM H4 1 123.300 418.400 +CM CM CT 1 119.700 585.760 +CM CM HA 1 119.700 418.400 +CM CM H4 1 119.700 418.400 +CM CM N* 1 121.200 585.760 +CM CM OS 1 125.000 669.440 +H4 CM N* 1 119.100 418.400 +H4 CM OS 1 113.000 418.400 +HA CM HA 1 120.000 292.880 +HA CM CD 1 120.000 418.400 +HA CM CT 1 120.000 418.400 +C CS CS 1 120.700 527.184 +C CS CT 1 119.700 585.760 +C CS HA 1 119.700 418.400 +C CS H4 1 119.700 418.400 +CA CS CS 1 117.000 527.184 +CA CS HA 1 123.300 418.400 +CA CS H4 1 123.300 418.400 +CM CS CT 1 119.700 585.760 +CS CS HA 1 119.700 418.400 +CS CS H4 1 119.700 418.400 +CS CS N* 1 121.200 585.760 +CS CS OS 1 125.000 669.440 +H4 CS N* 1 119.100 418.400 +H4 CS OS 1 113.000 418.400 +HA CS HA 1 120.000 292.880 +HA CS CD 1 120.000 418.400 +HA CS CT 1 120.000 418.400 +NC CQ NC 1 129.100 585.760 +H5 CQ NC 1 115.450 418.400 +H1 CT H1 1 109.500 292.880 +H1 CX H1 1 109.500 292.880 +H1 CT N* 1 109.500 418.400 +H1 CT OH 1 109.500 418.400 +H1 CT OS 1 109.500 418.400 +H1 CT CM 1 109.500 418.400 +H1 CT CS 1 109.500 418.400 +H1 CT CY 1 110.000 418.400 +H1 CT CZ 1 110.000 418.400 +H1 CT N 1 109.500 418.400 +H1 CX N 1 109.500 418.400 +H1 CT S 1 109.500 418.400 +H1 CT SH 1 109.500 418.400 +H1 CT N2 1 109.500 418.400 +H1 CT NT 1 109.500 418.400 +H2 CT H2 1 109.500 292.880 +H2 CT N* 1 109.500 418.400 +H2 CT OS 1 109.500 418.400 +HP CT HP 1 109.500 292.880 +HP CX HP 1 109.500 292.880 +HP CT N3 1 109.500 418.400 +HP CX N3 1 109.500 418.400 +HC CT HC 1 109.500 292.880 +HC CT CM 1 109.500 418.400 +HC CT CS 1 109.500 418.400 +HC CT CD 1 109.500 418.400 +HC CT CZ 1 110.000 418.400 +C CT H1 1 109.500 418.400 +C CX H1 1 109.500 418.400 +C CT HP 1 109.500 418.400 +C CX HP 1 109.500 418.400 +C CT HC 1 109.500 418.400 +C CT N 1 110.100 527.184 +C CX N 1 110.100 527.184 +C CT N3 1 111.200 669.440 +C CX N3 1 111.200 669.440 +C CT CT 1 111.100 527.184 +C CT CX 1 111.100 527.184 +C CX CT 1 111.100 527.184 +C CT OS 1 109.500 502.080 +CA CT HC 1 109.500 418.400 +CC CT CT 1 113.100 527.184 +CC CT CX 1 113.100 527.184 +CC CT HC 1 109.500 418.400 +CM CT CT 1 111.000 527.184 +CM CT OS 1 109.500 418.400 +CS CT CT 1 111.000 527.184 +CS CT OS 1 109.500 418.400 +CT CT CT 1 109.500 334.720 +CT CT CX 1 109.500 334.720 +CT CT HC 1 109.500 418.400 +CX CT HC 1 109.500 418.400 +CT CT H1 1 109.500 418.400 +CT CX H1 1 109.500 418.400 +CX CT H1 1 109.500 418.400 +CT CT H2 1 109.500 418.400 +CT CT HP 1 109.500 418.400 +CT CX HP 1 109.500 418.400 +CT CT N* 1 109.500 418.400 +CT CT OH 1 109.500 418.400 +CX CT OH 1 109.500 418.400 +CT CT OS 1 109.500 418.400 +CT CT S 1 114.700 418.400 +CX CT S 1 114.700 418.400 +CT CT SH 1 108.600 418.400 +CX CT SH 1 108.600 418.400 +CT CT CA 1 114.000 527.184 +CX CT CA 1 114.000 527.184 +CT CT N2 1 111.200 669.440 +CT CT N 1 109.700 669.440 +CT CX N 1 109.700 669.440 +CT CT N3 1 111.200 669.440 +CT CX N3 1 111.200 669.440 +CT CT NT 1 111.200 669.440 +CT CT CY 1 110.000 527.184 +CT CT CZ 1 110.000 527.184 +C* CT CT 1 115.600 527.184 +C* CT CX 1 115.600 527.184 +C* CT HC 1 109.500 418.400 +OS CT OS 1 101.000 1338.880 +OS CT CY 1 110.000 418.400 +OS CT CZ 1 110.000 418.400 +OS CT N* 1 109.500 418.400 +F CT F 1 109.100 644.336 +F CT H1 1 109.500 418.400 +F CT CT 1 109.000 418.400 +F CT H2 1 109.500 418.400 +Cl CT CT 1 108.500 418.400 +Cl CT H1 1 108.500 418.400 +Br CT CT 1 108.000 418.400 +Br CT H1 1 106.500 418.400 +I CT CT 1 106.000 418.400 +CT CC NA 1 120.000 585.760 +CT CC CV 1 120.000 585.760 +CT CC NB 1 120.000 585.760 +CV CC NA 1 120.000 585.760 +CW CC NA 1 120.000 585.760 +CW CC NB 1 120.000 585.760 +CT CC CW 1 120.000 585.760 +H5 CR NA 1 120.000 418.400 +H5 CR NB 1 120.000 418.400 +NA CR NA 1 120.000 585.760 +NA CR NB 1 120.000 585.760 +CC CV H4 1 120.000 418.400 +CC CV NB 1 120.000 585.760 +H4 CV NB 1 120.000 418.400 +CC CW H4 1 120.000 418.400 +CC CW NA 1 120.000 585.760 +C* CW H4 1 120.000 418.400 +C* CW NA 1 108.700 585.760 +H4 CW NA 1 120.000 418.400 +CB C* CT 1 128.600 585.760 +CB C* CW 1 106.400 527.184 +CT C* CW 1 125.000 585.760 +CA CN CB 1 122.700 527.184 +CA CN NA 1 132.800 585.760 +CB CN NA 1 104.400 585.760 +CT CY NY 1 180.000 669.440 +CT CZ CZ 1 180.000 669.440 +CZ CZ HZ 1 180.000 418.400 +C N CT 1 121.900 418.400 +C N CX 1 121.900 418.400 +C N H 1 120.000 418.400 +CT N H 1 118.040 418.400 +CX N H 1 118.040 418.400 +CT N CT 1 118.000 418.400 +CT N CX 1 118.000 418.400 +H N H 1 120.000 292.880 +C N* CM 1 121.600 585.760 +C N* CS 1 121.600 585.760 +C N* CT 1 117.600 585.760 +C N* H 1 119.200 418.400 +CB N* CK 1 105.400 585.760 +CB N* CP 1 105.400 585.760 +CB N* CT 1 125.800 585.760 +CB N* H 1 125.800 418.400 +CK N* CT 1 128.800 585.760 +CK N* H 1 128.800 418.400 +CP N* CT 1 128.800 585.760 +CP N* H 1 128.800 418.400 +CM N* CT 1 121.200 585.760 +CM N* H 1 121.200 418.400 +CS N* CT 1 121.200 585.760 +CS N* H 1 121.200 418.400 +CA N2 H 1 120.000 418.400 +CA N2 CT 1 123.200 418.400 +CT N2 H 1 118.400 418.400 +H N2 H 1 120.000 292.880 +CT N3 H 1 109.500 418.400 +CX N3 H 1 109.500 418.400 +CT N3 CT 1 109.500 418.400 +CT N3 CX 1 109.500 418.400 +H N3 H 1 109.500 292.880 +CT NT H 1 109.500 418.400 +CT NT CT 1 109.500 418.400 +H NT H 1 109.500 292.880 +C NA C 1 126.400 585.760 +C NA CA 1 125.200 585.760 +C NA H 1 116.800 418.400 +CA NA H 1 118.000 418.400 +CC NA CR 1 120.000 585.760 +CC NA H 1 120.000 418.400 +CR NA CW 1 120.000 585.760 +CR NA H 1 120.000 418.400 +CW NA H 1 120.000 418.400 +CN NA CW 1 111.600 585.760 +CN NA H 1 123.100 418.400 +CB NB CK 1 103.800 585.760 +CB NB CP 1 103.800 585.760 +CC NB CR 1 117.000 585.760 +CR NB CV 1 117.000 585.760 +C NC CA 1 120.500 585.760 +CA NC CB 1 112.200 585.760 +CA NC CQ 1 118.600 585.760 +CB NC CQ 1 111.000 585.760 +C OH HO 1 113.000 418.400 +CA OH HO 1 113.000 418.400 +CT OH HO 1 108.500 460.240 +HO OH P 1 108.500 376.560 +C OS CT 1 117.000 502.080 +CM OS CT 1 117.000 502.080 +CS OS CT 1 117.000 502.080 +CT OS CT 1 109.500 502.080 +CT OS P 1 120.500 836.800 +C OS P 1 120.500 836.800 +P OS P 1 120.500 836.800 +O2 P OH 1 108.230 376.560 +O2 P O2 1 119.900 1171.520 +OP P OP 1 119.900 1171.520 +OP P OS 1 108.230 836.800 +O2 P OS 1 108.230 836.800 +OH P OS 1 102.600 376.560 +OS P OS 1 102.600 376.560 +CT S CT 1 98.900 518.816 +CT S S 1 103.700 569.024 +CT SH HS 1 96.000 359.824 +HS SH HS 1 92.070 292.880 +CB NB EP 1 126.000 1255.200 +CC NB EP 1 126.000 1255.200 +CK NB EP 1 126.000 1255.200 +CP NB EP 1 126.000 1255.200 +CR NB EP 1 126.000 1255.200 +CV NB EP 1 126.000 1255.200 +C NC EP 1 120.000 1255.200 +CA NC EP 1 120.000 1255.200 +CB NC EP 1 120.000 1255.200 +CQ NC EP 1 120.000 1255.200 +CT N3 EP 1 109.500 1255.200 +H N3 EP 1 109.500 1255.200 +CT NT EP 1 109.500 1255.200 +H NT EP 1 109.500 1255.200 +C O EP 1 120.000 1255.200 +EP O EP 1 120.000 1255.200 +C OH EP 1 120.000 1255.200 +CT OH EP 1 109.500 1255.200 +HO OH EP 1 109.500 1255.200 +EP OH EP 1 109.500 1255.200 +C OS EP 1 109.500 1255.200 +CM OS EP 1 109.500 1255.200 +CS OS EP 1 109.500 1255.200 +CT OS EP 1 109.500 1255.200 +EP OS EP 1 109.500 1255.200 +CT S EP 1 90.000 1255.200 +CT SH EP 1 90.000 1255.200 +P OS EP 1 109.500 1255.200 +EP S EP 1 180.000 1255.200 +EP SH EP 1 180.000 1255.200 +HS SH EP 1 90.000 1255.200 +H1 CI CT 1 109.500 418.400 +H1 CI H1 1 109.500 292.880 +CI CT H1 1 109.500 418.400 +CI CT OS 1 109.500 418.400 +CI CT CT 1 109.500 334.720 +OS CI H1 1 109.500 418.400 +OS CI CT 1 109.500 418.400 +P OS CI 1 120.500 836.800 +OH CI H1 1 109.500 418.400 +OH CI CT 1 109.500 418.400 +HO OH CI 1 108.500 460.240 +H5 C5 N* 1 123.050 418.400 +H5 C5 NB 1 123.050 418.400 +N* C5 NB 1 113.900 585.760 +CB N* C5 1 105.400 585.760 +C5 N* CT 1 128.800 585.760 +CB NB C5 1 103.800 585.760 +C4 C NA 1 114.100 585.760 +C4 C O 1 125.300 669.440 +C4 CA N2 1 120.100 585.760 +C4 CA NC 1 121.500 585.760 +C C4 C4 1 120.700 527.184 +C C4 CT 1 119.700 585.760 +C C4 HA 1 119.700 418.400 +C C4 H4 1 119.700 418.400 +CA C4 C4 1 117.000 527.184 +CA C4 HA 1 123.300 418.400 +CA C4 H4 1 123.300 418.400 +C4 C4 CT 1 119.700 585.760 +C4 C4 HA 1 119.700 418.400 +C4 C4 H4 1 119.700 418.400 +C4 C4 N* 1 121.200 585.760 +H4 C4 N* 1 119.100 418.400 +H1 CT C4 1 109.500 418.400 +HC CT C4 1 109.500 418.400 +C N* C4 1 121.600 585.760 +C4 N* CT 1 121.200 585.760 +EP S S 1 96.700 1255.200 +N C 2C 1 116.600 585.760 +O C 2C 1 120.400 669.440 +OH C 2C 1 110.000 669.440 +CB C* 2C 1 128.600 585.760 +CW C* 2C 1 125.000 585.760 +C8 C8 C8 1 109.500 334.720 +C8 C8 CX 1 109.500 334.720 +C8 C8 H1 1 109.500 418.400 +C8 C8 HC 1 109.500 418.400 +C8 C8 HP 1 109.500 418.400 +C8 C8 N2 1 111.200 669.440 +C8 C8 N3 1 111.200 669.440 +CX C8 HC 1 109.500 418.400 +H1 C8 H1 1 109.500 292.880 +H1 C8 N2 1 109.500 418.400 +HC C8 HC 1 109.500 292.880 +HP C8 HP 1 109.500 292.880 +HP C8 N3 1 109.500 418.400 +CA CA 2C 1 120.000 585.760 +CV CC 2C 1 120.000 585.760 +CW CC 2C 1 120.000 585.760 +NA CC 2C 1 120.000 585.760 +NB CC 2C 1 120.000 585.760 +O2 CO O2 1 126.000 669.440 +O2 CO 2C 1 117.000 585.760 +HC CT 2C 1 109.500 418.400 +HC CT 3C 1 109.500 418.400 +C CX C8 1 111.100 527.184 +C CX 2C 1 111.100 527.184 +C CX 3C 1 111.100 527.184 +C8 CX H1 1 109.500 418.400 +C8 CX N 1 109.700 669.440 +C8 CX N3 1 111.200 669.440 +H1 CX 2C 1 109.500 418.400 +H1 CX 3C 1 109.500 418.400 +HP CX C8 1 109.500 418.400 +HP CX 2C 1 109.500 418.400 +HP CX 3C 1 109.500 418.400 +N CX 2C 1 109.700 669.440 +N CX 3C 1 109.700 669.440 +N3 CX 2C 1 111.200 669.440 +N3 CX 3C 1 111.200 669.440 +C8 N2 CA 1 123.200 418.400 +C8 N2 H 1 118.400 418.400 +C8 N3 H 1 109.500 418.400 +HO OH 2C 1 108.500 460.240 +HO OH 3C 1 108.500 460.240 +CT S 2C 1 98.900 518.816 +2C S S 1 103.700 569.024 +HS SH 2C 1 96.000 359.824 +C 2C CX 1 111.100 527.184 +C 2C HC 1 109.500 418.400 +C 2C 2C 1 111.100 527.184 +C* 2C CX 1 115.600 527.184 +C* 2C HC 1 109.500 418.400 +CA 2C CX 1 114.000 527.184 +CA 2C HC 1 109.500 418.400 +CC 2C CX 1 113.100 527.184 +CC 2C HC 1 109.500 418.400 +CO 2C CX 1 111.100 527.184 +CO 2C HC 1 109.500 418.400 +CO 2C 2C 1 111.100 527.184 +CT 2C HC 1 109.500 418.400 +CT 2C 3C 1 109.500 334.720 +CX 2C H1 1 109.500 418.400 +CX 2C HC 1 109.500 418.400 +CX 2C OH 1 109.500 418.400 +CX 2C S 1 114.700 418.400 +CX 2C SH 1 108.600 418.400 +CX 2C 2C 1 109.500 334.720 +CX 2C 3C 1 109.500 334.720 +H1 2C H1 1 109.500 292.880 +H1 2C OH 1 109.500 418.400 +H1 2C S 1 109.500 418.400 +H1 2C SH 1 109.500 418.400 +H1 2C 2C 1 109.500 418.400 +HC 2C HC 1 109.500 292.880 +HC 2C 2C 1 109.500 418.400 +HC 2C 3C 1 109.500 418.400 +S 2C 2C 1 114.700 418.400 +CT 3C CT 1 109.500 334.720 +CT 3C CX 1 109.500 334.720 +CT 3C H1 1 109.500 418.400 +CT 3C HC 1 109.500 418.400 +CT 3C OH 1 109.500 418.400 +CT 3C 2C 1 109.500 334.720 +CX 3C H1 1 109.500 418.400 +CX 3C HC 1 109.500 418.400 +CX 3C OH 1 109.500 418.400 +CX 3C 2C 1 109.500 334.720 +H1 3C OH 1 109.500 418.400 +HC 3C 2C 1 109.500 418.400 + + +[ dihedraltypes ] ; improper +;i j k l func phase kd pn +Br CA CA CA 4 180.00 4.60240 2 +C4 N2 CA NC 4 180.00 4.60240 2 +CA CA CA 2C 4 180.00 4.60240 2 +CA CA CA CT 4 180.00 4.60240 2 +CA CA CA OH 4 180.00 4.60240 2 +CA CA C OH 4 180.00 4.60240 2 +CA CA C OS 4 180.00 4.60240 2 +CB C5 N* CT 4 180.00 4.18400 2 +CB CK N* CT 4 180.00 4.18400 2 +CB CP N* CT 4 180.00 4.18400 2 +CB CT C* CW 4 180.00 4.60240 2 +CB N2 CA NC 4 180.00 4.60240 2 +C C4 C4 CT 4 180.00 4.60240 2 +C C4 N* CT 4 180.00 4.18400 2 +C CM CM CT 4 180.00 4.60240 2 +C CM N* CT 4 180.00 4.18400 2 +C CS CM CT 4 180.00 4.60240 2 +C CS CS CT 4 180.00 4.60240 2 +C CS N* CT 4 180.00 4.18400 2 +C CT N H 4 180.00 4.60240 2 +C CT N O 4 180.00 4.60240 2 +C CX N H 4 180.00 4.60240 2 +CM CT CM HA 4 180.00 4.60240 2 +CM H4 C O 4 180.00 4.60240 2 +CM N2 CA NC 4 180.00 4.60240 2 +CR CC NA P 4 180.00 4.60240 2 +CS CT CS HA 4 180.00 4.60240 2 +CS H4 C O 4 180.00 4.60240 2 +CS N2 CA NC 4 180.00 4.60240 2 +CT CV CC NA 4 180.00 4.60240 2 +CT CW CC NA 4 180.00 4.60240 2 +NB CW CC CT 4 180.00 4.60240 2 +CT CW CC NB 4 180.00 4.60240 2 +CT O C OH 4 180.00 43.93200 2 +H5 O C OH 4 180.00 4.60240 2 +H5 O C OS 4 180.00 4.60240 2 +N2 NA CA NC 4 180.00 4.60240 2 +2C O C OH 4 180.00 43.93200 2 +X CT N CT 4 180.00 4.18400 2 +X CT N CX 4 180.00 4.18400 2 +X N2 CA N2 4 180.00 43.93200 2 +X O2 C O2 4 180.00 43.93200 2 +X O2 CO O2 4 180.00 43.93200 2 +X X C4 H4 4 180.00 4.60240 2 +X X C4 HA 4 180.00 4.60240 2 +X X C5 H5 4 180.00 4.60240 2 +X X CA H4 4 180.00 4.60240 2 +X X CA H5 4 180.00 4.60240 2 +X X CA HA 4 180.00 4.60240 2 +X X CK H5 4 180.00 4.60240 2 +X X CM H4 4 180.00 4.60240 2 +X X CM HA 4 180.00 4.60240 2 +X X C O 4 180.00 43.93200 2 +X X CP H5 4 180.00 4.60240 2 +X X CQ H5 4 180.00 4.60240 2 +X X CR H5 4 180.00 4.60240 2 +X X CS H4 4 180.00 4.60240 2 +X X CS HA 4 180.00 4.60240 2 +X X CV H4 4 180.00 4.60240 2 +X X CW H4 4 180.00 4.60240 2 +X X N2 H 4 180.00 4.18400 2 +X X NA H 4 180.00 4.18400 2 +X X N H 4 180.00 4.18400 2 + + +[ dihedraltypes ] +;i j k l func + 3C CX N C 9 0.0 0.00000 4 + 3C CX N C 9 0.0 3.34720 3 + 3C CX N C 9 0.0 7.53120 2 + 3C CX N C 9 0.0 8.36800 1 + 2C 2C S CT 9 0.0 0.23849 4 + 2C 2C S CT 9 0.0 1.73218 3 + 2C 2C S CT 9 0.0 1.84933 2 + 2C 2C S CT 9 180.0 1.03345 1 + 2C 2C CO O2 9 0.0 0.26778 4 + 2C 2C CO O2 9 180.0 1.63176 2 + 2C 2C C OH 9 180.0 0.27614 4 + 2C 2C C OH 9 180.0 0.10460 3 + 2C 2C C OH 9 180.0 4.61914 2 + 2C 2C C OH 9 180.0 3.44762 1 + 2C 2C C O 9 0.0 0.00000 1 + 2C 2C C N 9 0.0 0.17573 4 + 2C 2C C N 9 180.0 0.35564 3 + 2C 2C C N 9 180.0 3.53548 2 + 2C 2C C N 9 180.0 2.54806 1 + 2C S S 2C 9 0.0 1.58574 4 + 2C S S 2C 9 0.0 2.85349 3 + 2C S S 2C 9 0.0 18.74432 2 + 2C S S 2C 9 0.0 1.75728 1 + 2C CX N C 9 0.0 0.00000 4 + 2C CX N C 9 0.0 3.34720 3 + 2C CX N C 9 0.0 7.53120 2 + 2C CX N C 9 0.0 8.36800 1 + 2C C OH HO 9 0.0 0.47279 4 + 2C C OH HO 9 0.0 2.00414 3 + 2C C OH HO 9 180.0 11.32190 2 + 2C C OH HO 9 180.0 1.87443 1 + 2C CC NB CR 9 180.0 10.04160 2 + 2C CC NA H 9 180.0 5.85760 2 + 2C CC NA CR 9 180.0 5.85760 2 + 2C CC CW NA 9 180.0 22.48900 2 + 2C CC CW H4 9 180.0 22.48900 2 + 2C CC CV NB 9 180.0 21.54760 2 + 2C CC CV H4 9 180.0 21.54760 2 + CX 3C OH HO 9 0.0 0.05439 4 + CX 3C OH HO 9 0.0 0.98742 3 + CX 3C OH HO 9 0.0 1.05018 2 + CX 3C OH HO 9 180.0 0.02510 1 + CX 3C 2C CT 9 0.0 0.96232 4 + CX 3C 2C CT 9 0.0 0.44769 3 + CX 3C 2C CT 9 0.0 0.22175 2 + CX 3C 2C CT 9 0.0 1.87025 1 + CT 3C OH HO 9 0.0 0.20083 4 + CT 3C OH HO 9 0.0 0.98742 3 + CT 3C OH HO 9 180.0 0.33054 2 + CT 3C OH HO 9 0.0 2.69031 1 + CT 3C 2C CT 9 0.0 0.93722 4 + CT 3C 2C CT 9 0.0 0.44769 3 + CT 3C 2C CT 9 180.0 0.32217 2 + CT 3C 2C CT 9 0.0 0.84517 1 + HC 2C 3C HC 9 0.0 0.62760 3 + HC 2C 3C CX 9 0.0 0.66944 3 + HC 2C 3C CT 9 0.0 0.66944 3 + HC 2C 2C HC 9 0.0 0.62760 3 + CX 2C S S 9 180.0 0.56484 4 + CX 2C S S 9 0.0 1.26357 3 + CX 2C S S 9 0.0 2.78654 2 + CX 2C S S 9 0.0 0.23430 1 + CX 2C SH HS 9 0.0 0.12552 4 + CX 2C SH HS 9 0.0 1.05437 3 + CX 2C SH HS 9 0.0 2.56061 2 + CX 2C SH HS 9 0.0 0.38493 1 + CX 2C OH HO 9 0.0 0.02929 4 + CX 2C OH HO 9 0.0 1.11713 3 + CX 2C OH HO 9 0.0 1.85770 2 + CX 2C OH HO 9 0.0 0.88282 1 + CX 2C CO O2 9 180.0 0.12970 4 + CX 2C CO O2 9 0.0 0.00000 3 + CX 2C CO O2 9 180.0 3.21750 2 + CX 2C CO O2 9 0.0 0.00000 1 + CX 2C C OH 9 180.0 0.83262 4 + CX 2C C OH 9 0.0 0.03347 3 + CX 2C C OH 9 180.0 2.40580 2 + CX 2C C OH 9 180.0 5.01662 1 + CX 2C C O 9 0.0 0.00000 1 + CX 2C C N 9 0.0 0.03347 4 + CX 2C C N 9 180.0 1.25938 3 + CX 2C C N 9 180.0 2.02924 2 + CX 2C C N 9 180.0 3.46435 1 + CX 2C 3C HC 9 0.0 0.66944 3 + CX 2C 3C CT 9 0.0 0.74894 4 + CX 2C 3C CT 9 0.0 0.59413 3 + CX 2C 3C CT 9 180.0 0.11297 2 + CX 2C 3C CT 9 0.0 1.58574 1 + CX 2C 2C S 9 0.0 0.11715 4 + CX 2C 2C S 9 0.0 0.06694 3 + CX 2C 2C S 9 0.0 1.02508 2 + CX 2C 2C S 9 0.0 1.74473 1 + CX 2C 2C HC 9 0.0 0.66944 3 + CX 2C 2C CO 9 180.0 0.23430 4 + CX 2C 2C CO 9 180.0 2.54387 3 + CX 2C 2C CO 9 180.0 0.92885 2 + CX 2C 2C CO 9 180.0 5.71953 1 + CX 2C 2C C 9 0.0 0.57739 4 + CX 2C 2C C 9 180.0 1.72381 3 + CX 2C 2C C 9 0.0 0.34727 2 + CX 2C 2C C 9 180.0 0.82006 1 + CT 2C 3C HC 9 0.0 0.66944 3 + OS P OS CT 9 0.0 1.04600 3 + OS P OS CT 9 0.0 5.02080 2 + OS P OS CI 9 357.2 1.48473 3 + OS P OS CI 9 352.0 5.25733 2 + OS P OS CI 9 31.8 0.77480 1 + OS CT N* CS 9 16.0 1.47059 4 + OS CT N* CS 9 179.3 2.43300 3 + OS CT N* CS 9 16.8 7.31681 2 + OS CT N* CS 9 149.9 4.28919 1 + OS CT N* CP 9 4.0 1.07119 4 + OS CT N* CP 9 168.7 1.85238 3 + OS CT N* CP 9 6.2 4.45788 2 + OS CT N* CP 9 74.8 2.95014 1 + OS CT N* CM 9 0.0 0.00000 2 + OS CT N* CM 9 0.0 10.46000 1 + OS CT N* CK 9 0.0 0.00000 2 + OS CT N* CK 9 0.0 10.46000 1 + OS CT N* C5 9 19.1 1.29357 4 + OS CT N* C5 9 171.6 1.91435 3 + OS CT N* C5 9 15.6 4.49374 2 + OS CT N* C5 9 68.8 4.04011 1 + OS CT N* C4 9 32.2 1.29842 4 + OS CT N* C4 9 185.9 3.92237 3 + OS CT N* C4 9 16.5 6.83912 2 + OS CT N* C4 9 147.0 5.12565 1 + OS CT CT OS 9 0.0 0.60250 3 + OS CT CT OS 9 0.0 4.91620 2 + OS CT CT OH 9 0.0 0.60250 3 + OS CT CT OH 9 0.0 4.91620 2 + OP P OS CA 9 180.0 0.00000 1 + OH P OS CT 9 0.0 1.04600 3 + OH P OS CT 9 0.0 5.02080 2 + OH P OS CI 9 357.2 1.48473 3 + OH P OS CI 9 352.0 5.25733 2 + OH P OS CI 9 31.8 0.77480 1 + OH CT CT OH 9 0.0 0.60250 3 + OH CT CT OH 9 0.0 4.91620 2 + OH C 2C HC 9 0.0 0.00000 2 + O C OS CT 9 180.0 11.29680 2 + O C OS CT 9 180.0 5.85760 1 + O C N EP 9 180.0 0.00000 2 + O C 2C HC 9 180.0 0.33472 3 + O C 2C HC 9 0.0 0.00000 2 + O C 2C HC 9 0.0 3.34720 1 + O2 CO 2C HC 9 0.0 0.00000 2 + N CX CT CC 9 0.0 0.37238 4 + N CX CT CC 9 0.0 0.91630 3 + N CX CT CC 9 180.0 0.92466 2 + N CX CT CC 9 180.0 1.28030 1 + N CX CT CA 9 180.0 0.02929 4 + N CX CT CA 9 0.0 0.80333 3 + N CX CT CA 9 180.0 1.21336 2 + N CX CT CA 9 180.0 0.05021 1 + N CX CT C* 9 0.0 0.12970 4 + N CX CT C* 9 0.0 0.97906 3 + N CX CT C* 9 180.0 1.30959 2 + N CX CT C* 9 0.0 0.33054 1 + N CX C N 9 0.0 0.00000 4 + N CX C N 9 180.0 2.30120 3 + N CX C N 9 180.0 6.61072 2 + N CX C N 9 180.0 1.88280 1 + N CX C8 C8 9 0.0 0.65084 3 + N CX 3C OH 9 0.0 0.39748 4 + N CX 3C OH 9 0.0 1.31796 3 + N CX 3C OH 9 0.0 0.02510 2 + N CX 3C OH 9 0.0 2.82002 1 + N CX 3C CT 9 180.0 0.00418 4 + N CX 3C CT 9 0.0 0.61923 3 + N CX 3C CT 9 180.0 0.90374 2 + N CX 3C CT 9 0.0 1.41001 1 + N CX 3C 2C 9 180.0 0.40585 4 + N CX 3C 2C 9 0.0 0.47279 3 + N CX 3C 2C 9 180.0 0.60250 2 + N CX 3C 2C 9 0.0 1.29704 1 + N CX 2C SH 9 0.0 0.13807 4 + N CX 2C SH 9 0.0 1.05018 3 + N CX 2C SH 9 180.0 2.03342 2 + N CX 2C SH 9 0.0 0.64434 1 + N CX 2C S 9 0.0 0.26778 4 + N CX 2C S 9 0.0 1.35143 3 + N CX 2C S 9 180.0 0.08786 2 + N CX 2C S 9 0.0 1.96230 1 + N CX 2C OH 9 0.0 0.66944 4 + N CX 2C OH 9 0.0 1.67778 3 + N CX 2C OH 9 180.0 1.02926 2 + N CX 2C OH 9 0.0 2.78654 1 + N CX 2C CO 9 0.0 0.37238 4 + N CX 2C CO 9 0.0 0.24267 3 + N CX 2C CO 9 180.0 2.70705 2 + N CX 2C CO 9 180.0 9.01234 1 + N CX 2C C 9 0.0 0.24686 4 + N CX 2C C 9 0.0 0.13807 3 + N CX 2C C 9 180.0 1.24265 2 + N CX 2C C 9 180.0 2.87859 1 + N CX 2C 3C 9 0.0 0.30543 4 + N CX 2C 3C 9 0.0 0.60250 3 + N CX 2C 3C 9 180.0 1.08366 2 + N CX 2C 3C 9 0.0 0.41003 1 + N CX 2C 2C 9 0.0 0.32635 4 + N CX 2C 2C 9 0.0 0.60250 3 + N CX 2C 2C 9 180.0 0.76986 2 + N CX 2C 2C 9 180.0 0.41840 1 + N CT CT OH 9 0.0 0.00000 4 + N CT CT OH 9 0.0 0.65270 3 + N CT CT OH 9 0.0 6.23416 2 + N CT CT OH 9 0.0 0.00000 1 + N C CX CT 9 0.0 0.00000 4 + N C CX CT 9 0.0 1.67360 3 + N C CX CT 9 0.0 0.83680 2 + N C CX CT 9 0.0 0.83680 1 + N C CX C8 9 0.0 0.00000 4 + N C CX C8 9 0.0 1.67360 3 + N C CX C8 9 0.0 0.83680 2 + N C CX C8 9 0.0 0.83680 1 + N C CX 3C 9 0.0 0.00000 4 + N C CX 3C 9 0.0 1.67360 3 + N C CX 3C 9 0.0 0.83680 2 + N C CX 3C 9 0.0 0.83680 1 + N C CX 2C 9 0.0 0.00000 4 + N C CX 2C 9 0.0 1.67360 3 + N C CX 2C 9 0.0 0.83680 2 + N C CX 2C 9 0.0 0.83680 1 + N C 2C HC 9 0.0 0.00000 2 + NB CC 2C HC 9 0.0 0.00000 2 + NA CC 2C HC 9 0.0 0.00000 2 + N3 CX CT CC 9 0.0 0.37238 4 + N3 CX CT CC 9 0.0 0.91630 3 + N3 CX CT CC 9 180.0 0.92466 2 + N3 CX CT CC 9 180.0 1.28030 1 + N3 CX CT CA 9 180.0 0.02929 4 + N3 CX CT CA 9 0.0 0.80333 3 + N3 CX CT CA 9 180.0 1.21336 2 + N3 CX CT CA 9 180.0 0.05021 1 + N3 CX CT C* 9 0.0 0.12970 4 + N3 CX CT C* 9 0.0 0.97906 3 + N3 CX CT C* 9 180.0 1.30959 2 + N3 CX CT C* 9 0.0 0.33054 1 + N3 CX C8 C8 9 0.0 0.65084 3 + N3 CX 3C OH 9 0.0 0.39748 4 + N3 CX 3C OH 9 0.0 1.31796 3 + N3 CX 3C OH 9 0.0 0.02510 2 + N3 CX 3C OH 9 0.0 2.82002 1 + N3 CX 3C CT 9 180.0 0.00418 4 + N3 CX 3C CT 9 0.0 0.61923 3 + N3 CX 3C CT 9 180.0 0.90374 2 + N3 CX 3C CT 9 0.0 1.41001 1 + N3 CX 3C 2C 9 180.0 0.40585 4 + N3 CX 3C 2C 9 0.0 0.47279 3 + N3 CX 3C 2C 9 180.0 0.60250 2 + N3 CX 3C 2C 9 0.0 1.29704 1 + N3 CX 2C SH 9 0.0 0.13807 4 + N3 CX 2C SH 9 0.0 1.05018 3 + N3 CX 2C SH 9 180.0 2.03342 2 + N3 CX 2C SH 9 0.0 0.64434 1 + N3 CX 2C S 9 0.0 0.26778 4 + N3 CX 2C S 9 0.0 1.35143 3 + N3 CX 2C S 9 180.0 0.08786 2 + N3 CX 2C S 9 0.0 1.96230 1 + N3 CX 2C OH 9 0.0 0.66944 4 + N3 CX 2C OH 9 0.0 1.67778 3 + N3 CX 2C OH 9 180.0 1.02926 2 + N3 CX 2C OH 9 0.0 2.78654 1 + N3 CX 2C CO 9 0.0 0.37238 4 + N3 CX 2C CO 9 0.0 0.24267 3 + N3 CX 2C CO 9 180.0 2.70705 2 + N3 CX 2C CO 9 180.0 9.01234 1 + N3 CX 2C C 9 0.0 0.24686 4 + N3 CX 2C C 9 0.0 0.13807 3 + N3 CX 2C C 9 180.0 1.24265 2 + N3 CX 2C C 9 180.0 2.87859 1 + N3 CX 2C 3C 9 0.0 0.30543 4 + N3 CX 2C 3C 9 0.0 0.60250 3 + N3 CX 2C 3C 9 180.0 1.08366 2 + N3 CX 2C 3C 9 0.0 0.41003 1 + N3 CX 2C 2C 9 0.0 0.32635 4 + N3 CX 2C 2C 9 0.0 0.60250 3 + N3 CX 2C 2C 9 180.0 0.76986 2 + N3 CX 2C 2C 9 180.0 0.41840 1 + HO OH CT CX 9 0.0 0.66944 3 + HO OH CT CX 9 0.0 1.04600 1 + HO OH CT CT 9 0.0 0.66944 3 + HO OH CT CT 9 0.0 1.04600 1 + HO OH C O 9 180.0 9.62320 2 + HO OH C O 9 0.0 7.94960 1 + HO OH 3C H1 9 0.0 0.69733 3 + HO OH 2C H1 9 0.0 0.69733 3 + H N C O 9 180.0 10.46000 2 + H N C O 9 0.0 8.36800 1 + H N2 CA N2 9 0.0 0.00000 4 + H N2 CA N2 9 180.0 10.04160 2 + HC CT CT OS 9 0.0 0.00000 3 + HC CT CT OS 9 0.0 1.04600 1 + HC CT CT OH 9 0.0 0.00000 3 + HC CT CT OH 9 0.0 1.04600 1 + HC CT CT HC 9 0.0 0.62760 3 + HC CT CT F 9 0.0 0.00000 3 + HC CT CT F 9 0.0 0.79496 1 + HC CT CT CX 9 0.0 0.66944 3 + HC CT CT CT 9 0.0 0.66944 3 + HC CT CT Cl 9 0.0 0.00000 3 + HC CT CT Cl 9 0.0 1.04600 1 + HC CT CT Br 9 0.0 0.00000 3 + HC CT CT Br 9 0.0 2.30120 1 + HC CT CS CS 9 180.0 1.58992 3 + HC CT CS CS 9 0.0 4.81160 1 + HC CT C O 9 180.0 0.33472 3 + HC CT C O 9 0.0 0.00000 2 + HC CT C O 9 0.0 3.34720 1 + HC CT CM CM 9 180.0 1.58992 3 + HC CT CM CM 9 0.0 4.81160 1 + HC CT C4 C4 9 180.0 1.58992 3 + HC CT C4 C4 9 0.0 4.81160 1 + HC CT 3C OH 9 0.0 0.00000 3 + HC CT 3C OH 9 0.0 1.04600 1 + HC CT 3C HC 9 0.0 0.62760 3 + HC CT 3C H1 9 0.0 0.65084 3 + HC CT 3C CX 9 0.0 0.66944 3 + HC CT 3C CT 9 0.0 0.66944 3 + HC CT 3C 2C 9 0.0 0.66944 3 + HC CT 2C HC 9 0.0 0.62760 3 + HC CT 2C 3C 9 0.0 0.66944 3 + HC C8 C8 HC 9 0.0 0.62760 3 + HA CS OS EP 9 180.0 0.00000 2 + HA CM OS EP 9 180.0 0.00000 2 + H4 CS OS EP 9 180.0 0.00000 2 + H4 CM OS EP 9 180.0 0.00000 2 + H2 CT OS EP 9 0.0 0.00000 3 + H1 CX CT OH 9 0.0 0.00000 3 + H1 CX CT OH 9 0.0 1.04600 1 + H1 CX C O 9 180.0 0.33472 3 + H1 CX C O 9 0.0 0.00000 2 + H1 CX C O 9 0.0 3.34720 1 + H1 CX 3C OH 9 0.0 0.00000 3 + H1 CX 3C OH 9 0.0 1.04600 1 + H1 CX 2C OH 9 0.0 0.00000 3 + H1 CX 2C OH 9 0.0 1.04600 1 + H1 CT S 2C 9 0.0 1.39467 3 + H1 CT OS EP 9 0.0 0.00000 3 + H1 CT OH EP 9 0.0 0.00000 3 + H1 CT NT EP 9 0.0 0.00000 3 + H1 CT CT OS 9 0.0 0.00000 3 + H1 CT CT OS 9 0.0 1.04600 1 + H1 CT CT OH 9 0.0 0.00000 3 + H1 CT CT OH 9 0.0 1.04600 1 + H1 CT CT F 9 0.0 0.00000 3 + H1 CT CT F 9 0.0 0.79496 1 + H1 CT CT Cl 9 0.0 0.00000 3 + H1 CT CT Cl 9 0.0 1.04600 1 + H1 CT CT Br 9 0.0 0.00000 3 + H1 CT CT Br 9 0.0 2.30120 1 + H1 CT C O 9 180.0 0.33472 3 + H1 CT C O 9 0.0 0.00000 2 + H1 CT C O 9 0.0 3.34720 1 + H1 CT CI OS 9 0.0 1.04600 1 + H1 CT CI OH 9 0.0 1.04600 1 + H1 CI CT OS 9 0.0 1.04600 1 + H1 CI CT OH 9 0.0 1.04600 1 + F CT CT F 9 0.0 0.00000 3 + F CT CT F 9 180.0 5.02080 1 + EP S S EP 9 0.0 0.00000 3 + EP S S CT 9 0.0 0.00000 3 + EP S S 2C 9 0.0 0.00000 3 + CX CT CT CT 9 0.0 0.75312 3 + CX CT CT CT 9 180.0 1.04600 2 + CX CT CT CT 9 180.0 0.83680 1 + CX CT C N 9 0.0 0.00000 4 + CX CT C N 9 0.0 1.67360 3 + CX CT C N 9 0.0 0.83680 2 + CX CT C N 9 0.0 0.83680 1 + CX CT C* CW 9 0.0 0.00000 4 + CX CT C* CW 9 0.0 0.00000 3 + CX CT C* CW 9 0.0 0.00000 2 + CX CT C* CW 9 0.0 0.00000 1 + CX CT CC NB 9 180.0 0.19665 4 + CX CT CC NB 9 0.0 3.09616 3 + CX CT CC NB 9 0.0 0.85354 2 + CX CT CC NB 9 0.0 2.88696 1 + CX CT CC NA 9 180.0 0.15481 4 + CX CT CC NA 9 0.0 2.87022 3 + CX CT CC NA 9 180.0 1.64013 2 + CX CT CC NA 9 180.0 0.66944 1 + CX CT CC CV 9 180.0 0.04184 4 + CX CT CC CV 9 180.0 0.51045 3 + CX CT CC CV 9 0.0 3.13800 2 + CX CT CC CV 9 180.0 2.82002 1 + CX CT C* CB 9 180.0 0.39748 4 + CX CT C* CB 9 0.0 3.42670 3 + CX CT C* CB 9 0.0 1.70707 2 + CX CT C* CB 9 0.0 1.52716 1 + CX CT CA CA 9 180.0 0.20083 4 + CX CT CA CA 9 0.0 0.00000 3 + CX CT CA CA 9 180.0 0.28870 2 + CX CT CA CA 9 0.0 0.00000 1 + CX C8 C8 HC 9 0.0 0.66944 3 + CX C8 C8 C8 9 0.0 0.75312 3 + CX C8 C8 C8 9 180.0 1.04600 2 + CX C8 C8 C8 9 180.0 0.83680 1 + CW CC 2C HC 9 0.0 0.00000 2 + CW C* 2C HC 9 0.0 0.00000 2 + CV CC 2C HC 9 0.0 0.00000 2 + CT S S CT 9 0.0 2.51040 3 + CT S S CT 9 0.0 14.64400 2 + CT OS CT OS 9 0.0 0.41840 3 + CT OS CT OS 9 180.0 3.55640 2 + CT OS CT OS 9 180.0 5.64840 1 + CT OS CT N* 9 0.0 1.60247 3 + CT OS CT N* 9 0.0 2.71960 2 + CT OS CT CI 9 0.0 1.60247 3 + CT OS CT CI 9 180.0 0.41840 2 + CT CZ CZ HZ 9 0.0 0.00000 1 + CT CX N C 9 0.0 0.00000 4 + CT CX N C 9 0.0 3.34720 3 + CT CX N C 9 0.0 7.53120 2 + CT CX N C 9 0.0 8.36800 1 + CT CT OS EP 9 0.0 0.00000 3 + CT CT OS CT 9 0.0 1.60247 3 + CT CT OS CT 9 180.0 0.41840 2 + CT CT OS C 9 0.0 1.60247 3 + CT CT OS C 9 180.0 3.34720 1 + CT CT OH EP 9 0.0 0.00000 3 + CT CT NT EP 9 0.0 0.00000 3 + CT CT NT CT 9 0.0 1.25520 3 + CT CT NT CT 9 180.0 2.00832 2 + CT CT N C 9 0.0 0.00000 4 + CT CT N C 9 0.0 1.67360 3 + CT CT N C 9 0.0 8.36800 2 + CT CT N C 9 0.0 8.36800 1 + CT CT CT CT 9 0.0 0.75312 3 + CT CT CT CT 9 180.0 1.04600 2 + CT CT CT CT 9 180.0 0.83680 1 + CT CT C N 9 0.0 0.00000 4 + CT CT C N 9 0.0 1.67360 3 + CT CT C N 9 0.0 0.83680 2 + CT CT C N 9 0.0 0.83680 1 + CT CT CI OS 9 348.1 4.02848 3 + CT CT CI OS 9 295.6 0.38535 2 + CT CT CI OS 9 191.0 4.92892 1 + CT CT CI OH 9 348.1 4.02848 3 + CT CT CI OH 9 295.6 0.38535 2 + CT CT CI OH 9 191.0 4.92892 1 + CT CS CS CT 9 180.0 27.82360 2 + CT CS CS CT 9 180.0 7.94960 1 + CT C N EP 9 180.0 0.00000 2 + CT CM CM CT 9 180.0 27.82360 2 + CT CM CM CT 9 180.0 7.94960 1 + CS CS OS EP 9 180.0 0.00000 2 + CS CS C O 9 0.0 1.25520 3 + CS CS C O 9 180.0 9.10020 2 + CR NA P OP 9 0.0 0.00000 3 + C N CX C 9 0.0 0.00000 4 + C N CX C 9 0.0 1.75728 3 + C N CX C 9 0.0 1.12968 2 + C N CX C 9 0.0 0.00000 1 + CM CM OS EP 9 180.0 0.00000 2 + CM CM C O 9 0.0 1.25520 3 + CM CM C O 9 180.0 9.10020 2 + Cl CT CT Cl 9 0.0 0.00000 3 + Cl CT CT Cl 9 180.0 1.88280 1 + CI CT CT CT 9 0.0 0.75312 3 + CI CT CT CT 9 180.0 1.04600 2 + CI CT CT CT 9 180.0 0.83680 1 + C CX CT CC 9 0.0 0.10460 4 + C CX CT CC 9 0.0 0.91630 3 + C CX CT CC 9 180.0 1.02090 2 + C CX CT CC 9 180.0 0.59831 1 + C CX CT CA 9 180.0 0.05021 4 + C CX CT CA 9 0.0 0.80333 3 + C CX CT CA 9 180.0 1.96230 2 + C CX CT CA 9 0.0 0.23012 1 + C CX CT C* 9 0.0 0.30962 4 + C CX CT C* 9 0.0 0.97906 3 + C CX CT C* 9 180.0 1.47695 2 + C CX CT C* 9 180.0 0.07113 1 + C CX C8 C8 9 0.0 0.65084 3 + C CX 3C OH 9 0.0 0.65270 4 + C CX 3C OH 9 0.0 1.31796 3 + C CX 3C OH 9 180.0 0.49790 2 + C CX 3C OH 9 180.0 2.91625 1 + C CX 3C CT 9 0.0 0.46861 4 + C CX 3C CT 9 0.0 0.61923 3 + C CX 3C CT 9 180.0 1.20918 2 + C CX 3C CT 9 180.0 1.69870 1 + C CX 3C 2C 9 0.0 0.48116 4 + C CX 3C 2C 9 0.0 0.47279 3 + C CX 3C 2C 9 180.0 3.07524 2 + C CX 3C 2C 9 0.0 0.67781 1 + C CX 2C SH 9 0.0 0.31380 4 + C CX 2C SH 9 0.0 1.05018 3 + C CX 2C SH 9 180.0 1.41001 2 + C CX 2C SH 9 180.0 1.12550 1 + C CX 2C S 9 0.0 1.16315 4 + C CX 2C S 9 0.0 1.35143 3 + C CX 2C S 9 180.0 1.64850 2 + C CX 2C S 9 0.0 2.51877 1 + C CX 2C OH 9 0.0 0.53974 4 + C CX 2C OH 9 0.0 1.67778 3 + C CX 2C OH 9 180.0 0.91211 2 + C CX 2C OH 9 180.0 2.76562 1 + C CX 2C CO 9 0.0 0.64434 4 + C CX 2C CO 9 0.0 0.24267 3 + C CX 2C CO 9 180.0 1.92046 2 + C CX 2C CO 9 0.0 1.77402 1 + C CX 2C C 9 0.0 0.44769 4 + C CX 2C C 9 0.0 0.13807 3 + C CX 2C C 9 180.0 1.26775 2 + C CX 2C C 9 0.0 4.37646 1 + C CX 2C 3C 9 0.0 0.79496 4 + C CX 2C 3C 9 0.0 0.60250 3 + C CX 2C 3C 9 180.0 2.59408 2 + C CX 2C 3C 9 0.0 2.95390 1 + C CX 2C 2C 9 0.0 0.60668 4 + C CX 2C 2C 9 0.0 0.60250 3 + C CX 2C 2C 9 180.0 1.64431 2 + C CX 2C 2C 9 180.0 1.76146 1 + CC NA P OP 9 0.0 1.00416 3 + CB C* 2C HC 9 0.0 0.00000 2 + CA C OH HO 9 0.0 0.27196 4 + CA C OH HO 9 0.0 0.00000 3 + CA C OH HO 9 180.0 3.69447 2 + CA C OH HO 9 0.0 0.00000 1 + C8 N2 CA N2 9 0.0 0.00000 4 + C8 N2 CA N2 9 180.0 10.04160 2 + C8 CX N C 9 0.0 0.00000 4 + C8 CX N C 9 0.0 3.34720 3 + C8 CX N C 9 0.0 7.53120 2 + C8 CX N C 9 0.0 8.36800 1 + C8 C8 N3 H 9 0.0 0.65084 3 + C8 C8 N2 CA 9 0.0 0.00000 1 + C8 C8 C8 N3 9 0.0 0.65084 3 + C8 C8 C8 N2 9 0.0 0.65084 3 + C8 C8 C8 HC 9 0.0 0.66944 3 + C8 C8 C8 C8 9 0.0 0.75312 3 + C8 C8 C8 C8 9 180.0 1.04600 2 + C8 C8 C8 C8 9 180.0 0.83680 1 + C4 C4 C O 9 0.0 1.25520 3 + C4 C4 C O 9 180.0 9.10020 2 + Br CT CT Br 9 0.0 0.00000 3 + Br CT CT Br 9 180.0 0.00000 1 + X 2C 2C X 9 0.0 0.65084 3 + X SH 2C X 9 0.0 1.04600 3 + X S 2C X 9 0.0 1.39467 3 + X OS P X 9 0.0 1.04600 3 + X OH P X 9 0.0 1.04600 3 + X CX N X 9 0.0 0.00000 2 + X CX N3 X 9 0.0 0.65084 3 + X CX 3C X 9 0.0 0.65084 3 + X CX 2C X 9 0.0 0.65084 3 + X CW NA X 9 180.0 6.27600 2 + X CV NB X 9 180.0 10.04160 2 + X CT S X 9 0.0 1.39467 3 + X CT SH X 9 0.0 1.04600 3 + X CT OS X 9 0.0 1.60387 3 + X CT OH X 9 0.0 0.69733 3 + X CT N* X 9 0.0 0.00000 2 + X CT N X 9 0.0 0.00000 2 + X CT NT X 9 0.0 1.25520 3 + X CT N3 X 9 0.0 0.65084 3 + X CT N2 X 9 0.0 0.00000 3 + X CT CZ X 9 0.0 0.00000 1 + X CT CY X 9 0.0 0.00000 1 + X CT CX X 9 0.0 0.65084 3 + X CT CT X 9 0.0 0.65084 3 + X CS OS X 9 180.0 4.39320 2 + X CS N* X 9 180.0 7.74040 2 + X CS CT X 9 0.0 0.00000 3 + X CS CS X 9 180.0 27.82360 2 + X CR NB X 9 180.0 20.92000 2 + X CR NA X 9 180.0 9.72780 2 + X CQ NC X 9 180.0 28.45120 2 + X CP N* X 9 180.0 7.11280 2 + X CP NB X 9 180.0 41.84000 2 + X C O X 9 180.0 11.71520 2 + X C OS X 9 180.0 11.29680 2 + X C OH X 9 180.0 9.62320 2 + X C N* X 9 180.0 6.06680 2 + X C N X 9 180.0 10.46000 2 + X CN NA X 9 180.0 6.38060 2 + X C NC X 9 180.0 16.73600 2 + X C NA X 9 180.0 5.64840 2 + X CM OS X 9 180.0 4.39320 2 + X CM N* X 9 180.0 7.74040 2 + X CM CT X 9 0.0 0.00000 3 + X CM CM X 9 180.0 27.82360 2 + X CK N* X 9 180.0 7.11280 2 + X CK NB X 9 180.0 41.84000 2 + X CI OS X 9 0.0 1.60387 3 + X CI OH X 9 0.0 0.69733 3 + X CI CT X 9 0.0 0.65084 3 + X CD CT X 9 0.0 0.00000 2 + X CD CS X 9 180.0 27.82360 2 + X CD CM X 9 180.0 27.82360 2 + X CD CD X 9 180.0 4.18400 2 + X C CX X 9 0.0 0.00000 2 + X C C X 9 180.0 15.16700 2 + X C* CW X 9 180.0 27.30060 2 + X C* CT X 9 0.0 0.00000 2 + X C CT X 9 0.0 0.00000 2 + X C CS X 9 180.0 9.10020 2 + X CC NB X 9 180.0 10.04160 2 + X CC NA X 9 180.0 5.85760 2 + X C CM X 9 180.0 9.10020 2 + X CC CW X 9 180.0 22.48900 2 + X CC CV X 9 180.0 21.54760 2 + X CC CT X 9 0.0 0.00000 2 + X C* CB X 9 180.0 7.00820 2 + X C CB X 9 180.0 12.55200 2 + X C CA X 9 180.0 15.16700 2 + X C C4 X 9 180.0 9.10020 2 + X CB N* X 9 180.0 6.90360 2 + X CB NC X 9 180.0 17.36360 2 + X CB NB X 9 180.0 10.66920 2 + X CB CN X 9 180.0 12.55200 2 + X CB CB X 9 180.0 22.80280 2 + X CA OH X 9 180.0 3.76560 2 + X CA NC X 9 180.0 20.08320 2 + X CA NA X 9 180.0 6.27600 2 + X CA N2 X 9 180.0 10.04160 2 + X CA CT X 9 0.0 0.00000 2 + X CA CS X 9 180.0 10.66920 2 + X CA CN X 9 180.0 15.16700 2 + X CA CM X 9 180.0 10.66920 2 + X CA CB X 9 180.0 14.64400 2 + X CA CA X 9 180.0 15.16700 2 + X CA C4 X 9 180.0 10.66920 2 + X CA 2C X 9 0.0 0.00000 2 + X C8 N3 X 9 0.0 0.65084 3 + X C8 N2 X 9 0.0 0.00000 3 + X C8 CX X 9 0.0 0.65084 3 + X C8 C8 X 9 0.0 0.65084 3 + X C5 N* X 9 180.0 7.11280 2 + X C5 NB X 9 180.0 41.84000 2 + X C4 N* X 9 180.0 7.74040 2 + X C4 CT X 9 0.0 0.00000 3 + X C4 C4 X 9 180.0 27.82360 2 diff --git a/tests/test_files/assets/amber14sb.ff/ffnonbonded.itp b/tests/test_files/assets/amber14sb.ff/ffnonbonded.itp new file mode 100644 index 0000000..81db53e --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/ffnonbonded.itp @@ -0,0 +1,93 @@ +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 4.64693e-01 2.45414e-01 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CD 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CI 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CO 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CP 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CS 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CX 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CY 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CZ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C4 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C5 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C8 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +2C 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +3C 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HZ 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +I 53 126.9 0.0000 A 5.09595e-01 2.24604e-01 +Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01 +Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NT 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NY 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +OP 8 16.00 0.0000 A 3.29633e-01 7.11280e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 3.03797e-01 8.10369e-01 +Rb 37 85.47 0.0000 A 3.23040e-01 1.37161e+00 +Cs 55 132.91 0.0000 A 3.52084e-01 1.70096e+00 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +EP 0 0.00 0.0000 A 0.00000e+00 0.00000e+00 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/tests/test_files/assets/amber14sb.ff/forcefield.doc b/tests/test_files/assets/amber14sb.ff/forcefield.doc new file mode 100644 index 0000000..39f5316 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/forcefield.doc @@ -0,0 +1,12 @@ +AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) + +******************************************************************** +* Amber99sb-ildn is an improvement to Amber99SB by * +* Kresten Lindorff-Larsen and coworkers at D.E. Shaw Research, inc.* +* The primary publication (please cite it) is * +* Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., * +* Klepeis, J.L., Dror, R.O., Shaw, D.E., * +* Improved side-chain torsion potentials for the Amber ff99SB * +* protein force field, Proteins 78:1950–1958 (2010) * +******************************************************************** + diff --git a/tests/test_files/assets/amber14sb.ff/forcefield.itp b/tests/test_files/assets/amber14sb.ff/forcefield.itp new file mode 100644 index 0000000..13d9c85 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/forcefield.itp @@ -0,0 +1,23 @@ +******************************************************************** +* The original ffamber ports were written by Eric J. Sorin, * +* CSU Long Beach, Dept. of Chem & Biochem, and have now been * +* integrated with the standard gromacs distribution. * +* (Please don't blame Eric for errors we might have introduced.) * +* For the implementation/validation, please read/cite: * +* Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. * +* For related material and updates, please consult * +* http://chemistry.csulb.edu/ffamber/ * +******************************************************************** + +#define _FF_AMBER +#define _FF_AMBER12SB + +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.8333 + +#include "ffnonbonded.itp" +#include "ffbonded.itp" +#include "gbsa.itp" + + diff --git a/tests/test_files/assets/amber14sb.ff/gbsa.itp b/tests/test_files/assets/amber14sb.ff/gbsa.itp new file mode 100644 index 0000000..632e8cb --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/gbsa.itp @@ -0,0 +1,38 @@ +[ implicit_genborn_params ] + +; atype sar st pi gbr hct +;Br 0.1 1 1 0.125 0.85 ; H +C 0.172 1 1.554 0.1875 0.72 ; C +CA 0.18 1 1.037 0.1875 0.72 ; C +CB 0.172 0.012 1.554 0.1875 0.72 ; C +CC 0.172 1 1.554 0.1875 0.72 ; C +CN 0.172 0.012 1.554 0.1875 0.72 ; C +CR 0.18 1 1.073 0.1875 0.72 ; C +CT 0.18 1 1.276 0.190 0.72 ; C +CV 0.18 1 1.073 0.1875 0.72 ; C +CW 0.18 1 1.073 0.1875 0.72 ; C +C* 0.172 0.012 1.554 0.1875 0.72 ; C +H 0.1 1 1 0.115 0.85 ; H +HC 0.1 1 1 0.125 0.85 ; H +H1 0.1 1 1 0.125 0.85 ; H +HA 0.1 1 1 0.125 0.85 ; H +H4 0.1 1 1 0.115 0.85 ; H +H5 0.1 1 1 0.125 0.85 ; H +HO 0.1 1 1 0.105 0.85 ; H +HS 0.1 1 1 0.125 0.85 ; H +HP 0.1 1 1 0.125 0.85 ; H +N 0.155 1 1.028 0.17063 0.79 ; N +NA 0.155 1 1.028 0.17063 0.79 ; N +NB 0.155 1 1.215 0.17063 0.79 ; N +N2 0.16 1 1.215 0.17063 0.79 ; N +N3 0.16 1 1.215 0.1625 0.79 ; N +O 0.15 1 0.926 0.148 0.85 ; O +OH 0.152 1 1.080 0.1535 0.85 ; O +O2 0.17 1 0.922 0.148 0.85 ; O +S 0.18 1 1.121 0.1775 0.96 ; S +SH 0.18 1 1.121 0.1775 0.96 ; S + +; masscenters for vsites do not have gbsa parameters + +MNH3 0 0 0 0 0 +MCH3 0 0 0 0 0 diff --git a/tests/test_files/assets/amber14sb.ff/ions.itp b/tests/test_files/assets/amber14sb.ff/ions.itp new file mode 100644 index 0000000..fe13ab6 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/ions.itp @@ -0,0 +1,88 @@ +[ moleculetype ] +; molname nrexcl +IB+ 1 ; big positive ion + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 IB 1 IB+ IB 1 1.00000 + + +[ moleculetype ] +; molname nrexcl +CA 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 C0 1 CA CA 1 2.00000 + + +[ moleculetype ] +; molname nrexcl +CL 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 Cl 1 CL CL 1 -1.00000 + + +[ moleculetype ] +; molname nrexcl +NA 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 Na 1 NA NA 1 1.00000 + + +[ moleculetype ] +; molname nrexcl +MG 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 MG 1 MG MG 1 2.00000 + + +[ moleculetype ] +; molname nrexcl +K 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 K 1 K K 1 1.00000 + + +[ moleculetype ] +; molname nrexcl +RB 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 Rb 1 RB RB 1 1.00000 + + +[ moleculetype ] +; molname nrexcl +CS 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 Cs 1 CS CS 1 1.00000 + + +[ moleculetype ] +; molname nrexcl +LI 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 Li 1 LI LI 1 1.00000 + + +[ moleculetype ] +; molname nrexcl +ZN 1 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 Zn 1 ZN ZN 1 2.00000 diff --git a/tests/test_files/assets/amber14sb.ff/rna.arn b/tests/test_files/assets/amber14sb.ff/rna.arn new file mode 100644 index 0000000..ed58c40 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/rna.arn @@ -0,0 +1,8 @@ +RNA OP1 O1P +RNA OP2 O2P +RNA H2' H2'1 +RNA H2'' H2'2 +RNA H5' H5'1 +RNA H5'' H5'2 +RNA HO5' H5T +RNA HO3' H3T diff --git a/tests/test_files/assets/amber14sb.ff/rna.hdb b/tests/test_files/assets/amber14sb.ff/rna.hdb new file mode 100644 index 0000000..43aa32d --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/rna.hdb @@ -0,0 +1,205 @@ +RA5 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RA 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RA3 10 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +RAN 11 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +2 3 H6 N6 C6 C5 +1 1 H2 C2 N1 N3 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +DT5 9 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DT 8 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +DT3 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +3 4 H7 C7 C5 C6 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +2 6 H2' C2' C1' C3' +1 2 H3T O3' C3' C4' +RU5 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RU 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RU3 10 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +RUN 11 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +1 1 H3 N3 C4 C2 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +RG5 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RG 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RG3 10 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +RGN 11 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N9 C2' +1 1 H8 C8 N9 N7 +1 1 H1 N1 C6 C2 +2 3 H2 N2 C2 N1 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +RC5 10 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RC 9 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +RC3 10 +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' +RCN 11 +1 2 H5T O5' C5' C4' +2 6 H5' C5' O5' C4' +1 5 H4' C4' C5' O4' C3' +1 5 H1' C1' O4' N1 C2' +1 1 H6 C6 N1 C5 +1 1 H5 C5 C6 C4 +2 3 H4 N4 C4 C5 +1 5 H3' C3' C4' C2' O3' +1 5 H2'1 C2' C1' C3' O2' +1 2 HO'2 O2' C2' C1' +1 2 H3T O3' C3' C4' diff --git a/tests/test_files/assets/amber14sb.ff/rna.r2b b/tests/test_files/assets/amber14sb.ff/rna.r2b new file mode 100644 index 0000000..9893f43 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/rna.r2b @@ -0,0 +1,6 @@ +; rtp residue to rtp building block table +;GMX Force-field +A RA RA5 RA3 RAN +U RU RU5 RU3 RUN +C RC RC5 RC3 RCN +G RG RG5 RG3 RGN diff --git a/tests/test_files/assets/amber14sb.ff/rna.rtp b/tests/test_files/assets/amber14sb.ff/rna.rtp new file mode 100644 index 0000000..bf1a3dd --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/rna.rtp @@ -0,0 +1,1232 @@ +[ bondedtypes ] +; Col 1: Type of bond +; Col 2: Type of angles +; Col 3: Type of proper dihedrals +; Col 4: Type of improper dihedrals +; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. +; Col 6: Number of excluded neighbors for nonbonded interactions +; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 +; Col 8: Remove impropers over the same bond as a proper if it is 1 +; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih + 1 1 9 4 1 3 1 0 + + +; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's + + +[ RA5 ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.03940 9 + H1' H2 0.20070 10 + N9 N* -0.02510 11 + C8 C5 0.20060 12 + H8 H5 0.15530 13 + N7 NB -0.60730 14 + C5 CB 0.05150 15 + C6 CA 0.70090 16 + N6 N2 -0.90190 17 + H61 H 0.41150 18 + H62 H 0.41150 19 + N1 NC -0.76150 20 + C2 CQ 0.58750 21 + H2 H5 0.04730 22 + N3 NC -0.69970 23 + C4 CB 0.30530 24 + C3' CT 0.20220 25 + H3' H1 0.06150 26 + C2' CT 0.06700 27 + H2'1 H1 0.09720 28 + O2' OH -0.61390 29 + HO'2 HO 0.41860 30 + O3' OS -0.52460 31 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + +[ RA ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.03940 11 + H1' H2 0.20070 12 + N9 N* -0.02510 13 + C8 C5 0.20060 14 + H8 H5 0.15530 15 + N7 NB -0.60730 16 + C5 CB 0.05150 17 + C6 CA 0.70090 18 + N6 N2 -0.90190 19 + H61 H 0.41150 20 + H62 H 0.41150 21 + N1 NC -0.76150 22 + C2 CQ 0.58750 23 + H2 H5 0.04730 24 + N3 NC -0.69970 25 + C4 CB 0.30530 26 + C3' CT 0.20220 27 + H3' H1 0.06150 28 + C2' CT 0.06700 29 + H2'1 H1 0.09720 30 + O2' OH -0.61390 31 + HO'2 HO 0.41860 32 + O3' OS -0.52460 33 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + -O3' P + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + +[ RA3 ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.03940 11 + H1' H2 0.20070 12 + N9 N* -0.02510 13 + C8 C5 0.20060 14 + H8 H5 0.15530 15 + N7 NB -0.60730 16 + C5 CB 0.05150 17 + C6 CA 0.70090 18 + N6 N2 -0.90190 19 + H61 H 0.41150 20 + H62 H 0.41150 21 + N1 NC -0.76150 22 + C2 CQ 0.58750 23 + H2 H5 0.04730 24 + N3 NC -0.69970 25 + C4 CB 0.30530 26 + C3' CT 0.20220 27 + H3' H1 0.06150 28 + C2' CT 0.06700 29 + H2'1 H1 0.09720 30 + O2' OH -0.61390 31 + HO'2 HO 0.41860 32 + O3' OH -0.65410 33 + H3T HO 0.43760 34 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + -O3' P + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + +[ RAN ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.03940 9 + H1' H2 0.20070 10 + N9 N* -0.02510 11 + C8 C5 0.20060 12 + H8 H5 0.15530 13 + N7 NB -0.60730 14 + C5 CB 0.05150 15 + C6 CA 0.70090 16 + N6 N2 -0.90190 17 + H61 H 0.41150 18 + H62 H 0.41150 19 + N1 NC -0.76150 20 + C2 CQ 0.58750 21 + H2 H5 0.04730 22 + N3 NC -0.69970 23 + C4 CB 0.30530 24 + C3' CT 0.20220 25 + H3' H1 0.06150 26 + C2' CT 0.06700 27 + H2'1 H1 0.09720 28 + O2' OH -0.61390 29 + HO'2 HO 0.41860 30 + O3' OH -0.65410 31 + H3T HO 0.43760 32 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 N6 + C6 N1 + N6 H61 + N6 H62 + N1 C2 + C2 H2 + C2 N3 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + [ impropers ] + C4 C8 N9 C1' + C6 H61 N6 H62 + N9 N7 C8 H8 + N1 N3 C2 H2 + C5 N6 C6 N1 + + +[ RU5 ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.06740 9 + H1' H2 0.18240 10 + N1 N* 0.04180 11 + C6 CS -0.11260 12 + H6 H4 0.21880 13 + C5 CS -0.36350 14 + H5 HA 0.18110 15 + C4 C 0.59520 16 + O4 O -0.57610 17 + N3 NA -0.35490 18 + H3 H 0.31540 19 + C2 C 0.46870 20 + O2 O -0.54770 21 + C3' CT 0.20220 22 + H3' H1 0.06150 23 + C2' CT 0.06700 24 + H2'1 H1 0.09720 25 + O2' OH -0.61390 26 + HO'2 HO 0.41860 27 + O3' OS -0.52460 28 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + [ impropers ] + C2 C6 N1 C1' + C6 C4 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + +[ RU ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.06740 11 + H1' H2 0.18240 12 + N1 N* 0.04180 13 + C6 CS -0.11260 14 + H6 H4 0.21880 15 + C5 CS -0.36350 16 + H5 HA 0.18110 17 + C4 C 0.59520 18 + O4 O -0.57610 19 + N3 NA -0.35490 20 + H3 H 0.31540 21 + C2 C 0.46870 22 + O2 O -0.54770 23 + C3' CT 0.20220 24 + H3' H1 0.06150 25 + C2' CT 0.06700 26 + H2'1 H1 0.09720 27 + O2' OH -0.61390 28 + HO'2 HO 0.41860 29 + O3' OS -0.52460 30 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + -O3' P + [ impropers ] + C2 C6 N1 C1' + C6 C4 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + +[ RU3 ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.06740 11 + H1' H2 0.18240 12 + N1 N* 0.04180 13 + C6 CS -0.11260 14 + H6 H4 0.21880 15 + C5 CS -0.36350 16 + H5 HA 0.18110 17 + C4 C 0.59520 18 + O4 O -0.57610 19 + N3 NA -0.35490 20 + H3 H 0.31540 21 + C2 C 0.46870 22 + O2 O -0.54770 23 + C3' CT 0.20220 24 + H3' H1 0.06150 25 + C2' CT 0.06700 26 + H2'1 H1 0.09720 27 + O2' OH -0.61390 28 + HO'2 HO 0.41860 29 + O3' OH -0.65410 30 + H3T HO 0.43760 31 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + -O3' P + [ impropers ] + C2 C6 N1 C1' + C6 C4 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + +[ RUN ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.06740 9 + H1' H2 0.18240 10 + N1 N* 0.04180 11 + C6 CS -0.11260 12 + H6 H4 0.21880 13 + C5 CS -0.36350 14 + H5 HA 0.18110 15 + C4 C 0.59520 16 + O4 O -0.57610 17 + N3 NA -0.35490 18 + H3 H 0.31540 19 + C2 C 0.46870 20 + O2 O -0.54770 21 + C3' CT 0.20220 22 + H3' H1 0.06150 23 + C2' CT 0.06700 24 + H2'1 H1 0.09720 25 + O2' OH -0.61390 26 + HO'2 HO 0.41860 27 + O3' OH -0.65410 28 + H3T HO 0.43760 29 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 O4 + C4 N3 + N3 H3 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + [ impropers ] + C2 C6 N1 C1' + C6 C4 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C4 C2 N3 H3 + N1 C5 C6 H6 + + +[ RG5 ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.01910 9 + H1' H2 0.20060 10 + N9 N* 0.04920 11 + C8 CP 0.13740 12 + H8 H5 0.16400 13 + N7 NB -0.57090 14 + C5 CB 0.17440 15 + C6 C 0.47700 16 + O6 O -0.55970 17 + N1 NA -0.47870 18 + H1 H 0.34240 19 + C2 CA 0.76570 20 + N2 N2 -0.96720 21 + H21 H 0.43640 22 + H22 H 0.43640 23 + N3 NC -0.63230 24 + C4 CB 0.12220 25 + C3' CT 0.20220 26 + H3' H1 0.06150 27 + C2' CT 0.06700 28 + H2'1 H1 0.09720 29 + O2' OH -0.61390 30 + HO'2 HO 0.41860 31 + O3' OS -0.52460 32 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ RG ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.01910 11 + H1' H2 0.20060 12 + N9 N* 0.04920 13 + C8 CP 0.13740 14 + H8 H5 0.16400 15 + N7 NB -0.57090 16 + C5 CB 0.17440 17 + C6 C 0.47700 18 + O6 O -0.55970 19 + N1 NA -0.47870 20 + H1 H 0.34240 21 + C2 CA 0.76570 22 + N2 N2 -0.96720 23 + H21 H 0.43640 24 + H22 H 0.43640 25 + N3 NC -0.63230 26 + C4 CB 0.12220 27 + C3' CT 0.20220 28 + H3' H1 0.06150 29 + C2' CT 0.06700 30 + H2'1 H1 0.09720 31 + O2' OH -0.61390 32 + HO'2 HO 0.41860 33 + O3' OS -0.52460 34 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + -O3' P + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ RG3 ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.01910 11 + H1' H2 0.20060 12 + N9 N* 0.04920 13 + C8 CP 0.13740 14 + H8 H5 0.16400 15 + N7 NB -0.57090 16 + C5 CB 0.17440 17 + C6 C 0.47700 18 + O6 O -0.55970 19 + N1 NA -0.47870 20 + H1 H 0.34240 21 + C2 CA 0.76570 22 + N2 N2 -0.96720 23 + H21 H 0.43640 24 + H22 H 0.43640 25 + N3 NC -0.63230 26 + C4 CB 0.12220 27 + C3' CT 0.20220 28 + H3' H1 0.06150 29 + C2' CT 0.06700 30 + H2'1 H1 0.09720 31 + O2' OH -0.61390 32 + HO'2 HO 0.41860 33 + O3' OH -0.65410 34 + H3T HO 0.43760 35 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + -O3' P + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + +[ RGN ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.01910 9 + H1' H2 0.20060 10 + N9 N* 0.04920 11 + C8 CP 0.13740 12 + H8 H5 0.16400 13 + N7 NB -0.57090 14 + C5 CB 0.17440 15 + C6 C 0.47700 16 + O6 O -0.55970 17 + N1 NA -0.47870 18 + H1 H 0.34240 19 + C2 CA 0.76570 20 + N2 N2 -0.96720 21 + H21 H 0.43640 22 + H22 H 0.43640 23 + N3 NC -0.63230 24 + C4 CB 0.12220 25 + C3' CT 0.20220 26 + H3' H1 0.06150 27 + C2' CT 0.06700 28 + H2'1 H1 0.09720 29 + O2' OH -0.61390 30 + HO'2 HO 0.41860 31 + O3' OH -0.65410 32 + H3T HO 0.43760 33 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N9 + C1' C2' + N9 C8 + N9 C4 + C8 H8 + C8 N7 + N7 C5 + C5 C6 + C5 C4 + C6 O6 + C6 N1 + N1 H1 + N1 C2 + C2 N2 + C2 N3 + N2 H21 + N2 H22 + N3 C4 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + [ impropers ] + C4 C8 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N9 N7 C8 H8 + N2 N1 C2 N3 + + +[ RC5 ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.00660 9 + H1' H2 0.20290 10 + N1 N* -0.04840 11 + C6 C4 0.00530 12 + H6 H4 0.19580 13 + C5 C4 -0.52150 14 + H5 HA 0.19280 15 + C4 CA 0.81850 16 + N4 N2 -0.95300 17 + H41 H 0.42340 18 + H42 H 0.42340 19 + N3 NC -0.75840 20 + C2 C 0.75380 21 + O2 O -0.62520 22 + C3' CT 0.20220 23 + H3' H1 0.06150 24 + C2' CT 0.06700 25 + H2'1 H1 0.09720 26 + O2' OH -0.61390 27 + HO'2 HO 0.41860 28 + O3' OS -0.52460 29 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + +[ RC ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.00660 11 + H1' H2 0.20290 12 + N1 N* -0.04840 13 + C6 C4 0.00530 14 + H6 H4 0.19580 15 + C5 C4 -0.52150 16 + H5 HA 0.19280 17 + C4 CA 0.81850 18 + N4 N2 -0.95300 19 + H41 H 0.42340 20 + H42 H 0.42340 21 + N3 NC -0.75840 22 + C2 C 0.75380 23 + O2 O -0.62520 24 + C3' CT 0.20220 25 + H3' H1 0.06150 26 + C2' CT 0.06700 27 + H2'1 H1 0.09720 28 + O2' OH -0.61390 29 + HO'2 HO 0.41860 30 + O3' OS -0.52460 31 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + -O3' P + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + +[ RC3 ] + [ atoms ] + P P 1.16620 1 + O1P O2 -0.77600 2 + O2P O2 -0.77600 3 + O5' OS -0.49890 4 + C5' CI 0.05580 5 + H5'1 H1 0.06790 6 + H5'2 H1 0.06790 7 + C4' CT 0.10650 8 + H4' H1 0.11740 9 + O4' OS -0.35480 10 + C1' CT 0.00660 11 + H1' H2 0.20290 12 + N1 N* -0.04840 13 + C6 C4 0.00530 14 + H6 H4 0.19580 15 + C5 C4 -0.52150 16 + H5 HA 0.19280 17 + C4 CA 0.81850 18 + N4 N2 -0.95300 19 + H41 H 0.42340 20 + H42 H 0.42340 21 + N3 NC -0.75840 22 + C2 C 0.75380 23 + O2 O -0.62520 24 + C3' CT 0.20220 25 + H3' H1 0.06150 26 + C2' CT 0.06700 27 + H2'1 H1 0.09720 28 + O2' OH -0.61390 29 + HO'2 HO 0.41860 30 + O3' OH -0.65410 31 + H3T HO 0.43760 32 + [ bonds ] + P O1P + P O2P + P O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + -O3' P + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + +[ RCN ] + [ atoms ] + H5T HO 0.42950 1 + O5' OH -0.62230 2 + C5' CI 0.05580 3 + H5'1 H1 0.06790 4 + H5'2 H1 0.06790 5 + C4' CT 0.10650 6 + H4' H1 0.11740 7 + O4' OS -0.35480 8 + C1' CT 0.00660 9 + H1' H2 0.20290 10 + N1 N* -0.04840 11 + C6 C4 0.00530 12 + H6 H4 0.19580 13 + C5 C4 -0.52150 14 + H5 HA 0.19280 15 + C4 CA 0.81850 16 + N4 N2 -0.95300 17 + H41 H 0.42340 18 + H42 H 0.42340 19 + N3 NC -0.75840 20 + C2 C 0.75380 21 + O2 O -0.62520 22 + C3' CT 0.20220 23 + H3' H1 0.06150 24 + C2' CT 0.06700 25 + H2'1 H1 0.09720 26 + O2' OH -0.61390 27 + HO'2 HO 0.41860 28 + O3' OH -0.65410 29 + H3T HO 0.43760 30 + [ bonds ] + H5T O5' + O5' C5' + C5' H5'1 + C5' H5'2 + C5' C4' + C4' H4' + C4' O4' + C4' C3' + O4' C1' + C1' H1' + C1' N1 + C1' C2' + N1 C6 + N1 C2 + C6 H6 + C6 C5 + C5 H5 + C5 C4 + C4 N4 + C4 N3 + N4 H41 + N4 H42 + N3 C2 + C2 O2 + C3' H3' + C3' C2' + C3' O3' + C2' H2'1 + C2' O2' + O2' HO'2 + O3' H3T + [ impropers ] + C2 C6 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + C5 N4 C4 N3 + + diff --git a/tests/test_files/assets/amber14sb.ff/spc.itp b/tests/test_files/assets/amber14sb.ff/spc.itp new file mode 100644 index 0000000..1e7cae5 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/spc.itp @@ -0,0 +1,33 @@ +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW_spc 1 SOL OW 1 -0.82 15.99940 + 2 HW_spc 1 SOL HW1 1 0.41 1.00800 + 3 HW_spc 1 SOL HW2 1 0.41 1.00800 + +#ifndef FLEXIBLE + +[ settles ] +; OW funct doh dhh +1 1 0.1 0.16330 + +[ exclusions ] +1 2 3 +2 1 3 +3 1 2 + +#else + +[ bonds ] +; i j funct length force.c. +1 2 1 0.1 345000 0.1 345000 +1 3 1 0.1 345000 0.1 345000 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 109.47 383 109.47 383 + +#endif diff --git a/tests/test_files/assets/amber14sb.ff/spce.itp b/tests/test_files/assets/amber14sb.ff/spce.itp new file mode 100644 index 0000000..7c97bfe --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/spce.itp @@ -0,0 +1,33 @@ +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW_spc 1 SOL OW 1 -0.8476 15.99940 + 2 HW_spc 1 SOL HW1 1 0.4238 1.00800 + 3 HW_spc 1 SOL HW2 1 0.4238 1.00800 + +#ifndef FLEXIBLE + +[ settles ] +; OW funct doh dhh +1 1 0.1 0.16330 + +[ exclusions ] +1 2 3 +2 1 3 +3 1 2 + +#else + +[ bonds ] +; i j funct length force.c. +1 2 1 0.1 345000 0.1 345000 +1 3 1 0.1 345000 0.1 345000 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 109.47 383 109.47 383 + +#endif diff --git a/tests/test_files/assets/amber14sb.ff/tip3p.itp b/tests/test_files/assets/amber14sb.ff/tip3p.itp new file mode 100644 index 0000000..ced4ece --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/tip3p.itp @@ -0,0 +1,34 @@ +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW 1 SOL OW 1 -0.834 16.00000 + 2 HW 1 SOL HW1 1 0.417 1.00800 + 3 HW 1 SOL HW2 1 0.417 1.00800 + +#ifndef FLEXIBLE + +[ settles ] +; OW funct doh dhh +1 1 0.09572 0.15139 + +[ exclusions ] +1 2 3 +2 1 3 +3 1 2 + +#else + +[ bonds ] +; i j funct length force_constant +1 2 1 0.09572 502416.0 0.09572 502416.0 +1 3 1 0.09572 502416.0 0.09572 502416.0 + + +[ angles ] +; i j k funct angle force_constant +2 1 3 1 104.52 628.02 104.52 628.02 + +#endif diff --git a/tests/test_files/assets/amber14sb.ff/tip4p.itp b/tests/test_files/assets/amber14sb.ff/tip4p.itp new file mode 100644 index 0000000..3f926ca --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/tip4p.itp @@ -0,0 +1,55 @@ +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW_tip4p 1 SOL OW 1 0 16.00000 + 2 HW_tip4p 1 SOL HW1 1 0.52 1.00800 + 3 HW_tip4p 1 SOL HW2 1 0.52 1.00800 + 4 MW 1 SOL MW 1 -1.04 0.00000 + +#ifndef FLEXIBLE + +[ settles ] +; i funct doh dhh +1 1 0.09572 0.15139 + +#else + +[ bonds ] +; i j funct length force.c. +1 2 1 0.09572 502416.0 0.09572 502416.0 +1 3 1 0.09572 502416.0 0.09572 502416.0 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 104.52 628.02 104.52 628.02 + +#endif + + +[ virtual_sites3 ] +; Vsite from funct a b +4 1 2 3 1 0.128012065 0.128012065 + + +[ exclusions ] +1 2 3 4 +2 1 3 4 +3 1 2 4 +4 1 2 3 + + +; The position of the virtual site is computed as follows: +; +; O +; +; V +; +; H H +; +; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] +; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] +; +; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) diff --git a/tests/test_files/assets/amber14sb.ff/tip4pew.itp b/tests/test_files/assets/amber14sb.ff/tip4pew.itp new file mode 100644 index 0000000..571bec6 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/tip4pew.itp @@ -0,0 +1,56 @@ +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW_tip4pew 1 SOL OW 1 0 16.00000 + 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 + 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 + 4 MW 1 SOL MW 1 -1.04844 0.00000 + +#ifndef FLEXIBLE + +[ settles ] +; i funct doh dhh +1 1 0.09572 0.15139 + +#else +[ bonds ] +; i j funct length force.c. +1 2 1 0.09572 502416.0 0.09572 502416.0 +1 3 1 0.09572 502416.0 0.09572 502416.0 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 104.52 628.02 104.52 628.02 + +#endif + + +[ virtual_sites3 ] +; Vsite from funct a b +4 1 2 3 1 0.106676721 0.106676721 + + +[ exclusions ] +1 2 3 4 +2 1 3 4 +3 1 2 4 +4 1 2 3 + + +; The position of the virtual site is computed as follows: +; +; O +; +; V +; +; H H +; +; Ewald tip4p: +; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] +; 0.0125 nm / [ cos (52.26 deg) * 0.09572 nm ] +; then a = b = 0.5 * const = 0.106676721 +; +; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) diff --git a/tests/test_files/assets/amber14sb.ff/tip5p.itp b/tests/test_files/assets/amber14sb.ff/tip5p.itp new file mode 100644 index 0000000..c3120b0 --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/tip5p.itp @@ -0,0 +1,69 @@ +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW_tip5p 1 SOL OW 1 0 16.00000 + 2 HW_tip5p 1 SOL HW1 1 0.241 1.00800 + 3 HW_tip5p 1 SOL HW2 1 0.241 1.00800 + 4 MW 1 SOL LP1 1 -0.241 0.00000 + 5 MW 1 SOL LP2 1 -0.241 0.00000 + +#ifndef FLEXIBLE + +[ settles ] +; i funct doh dhh +1 1 0.09572 0.15139 + +#else + +[ bonds ] +; i j funct length force.c. +1 2 1 0.09572 502416.0 0.09572 502416.0 +1 3 1 0.09572 502416.0 0.09572 502416.0 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 104.52 628.02 104.52 628.02 + +#endif + + +[ virtual_sites3 ] +; Vsite from funct a b c +4 1 2 3 4 -0.344908262 -0.34490826 -6.4437903493 +5 1 2 3 4 -0.344908262 -0.34490826 6.4437903493 + + +[ exclusions ] +1 2 3 4 5 +2 1 3 4 5 +3 1 2 4 5 +4 1 2 3 5 +5 1 2 3 4 + + +; The positions of the vsites are computed as follows: +; +; LP1 LP2 +; +; O +; +; H1 H2 +; +; angle A (H1-O-H2) = 104.52 +; angle B (M1-O-M2) = 109.47 +; dist C (H-O) = 0.09572 nm +; dist D (M-O) = 0.070 nm +; +;atom x y z +;O 0.0 0.0 0.0 +;H1 0.585882276 0.756950327 0.0 +;H2 0.585882276 -0.756950327 0.0 +;M1 -0.404151276 0.0 0.571543301 +;M2 -0.404151276 0.0 -0.571543301 +; Dummy pos x4 = x1 + a4*(x2-x1) + b4*(x3-x1) + c4*((x2-x1) x (x3-x1)) +; Dummy pos x5 = x1 + a5*(x2-x1) + b5*(x3-x1) + c5*((x2-x1) x (x3-x1)) +; a4 = b4 = a5 = b5 = (D*cos(B/2)) / (2*C*cos(A/2)) = -0.34490826 +; c5 = -c4 = (D * sin(B/2))/ (C^2 * sin(A)) = 6.4437903 diff --git a/tests/test_files/assets/amber14sb.ff/urea.itp b/tests/test_files/assets/amber14sb.ff/urea.itp new file mode 100644 index 0000000..8cb346a --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/urea.itp @@ -0,0 +1,36 @@ +[ moleculetype ] +; molname nrexcl +URE 3 + +[ atoms ] + 1 C 1 URE C 1 0.880229 12.01000 ; amber C type + 2 O 1 URE O 2 -0.613359 16.00000 ; amber O type + 3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type + 4 H 1 URE H11 4 0.395055 1.00800 ; amber H type + 5 H 1 URE H12 5 0.395055 1.00800 ; amber H type + 6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type + 7 H 1 URE H21 7 0.395055 1.00800 ; amber H type + 8 H 1 URE H22 8 0.395055 1.00800 ; amber H type + +[ bonds ] + 1 2 + 1 3 + 1 6 + 3 4 + 3 5 + 6 7 + 6 8 +[ dihedrals ] +; ai aj ak al funct definition + 2 1 3 4 9 + 2 1 3 5 9 + 2 1 6 7 9 + 2 1 6 8 9 + 3 1 6 7 9 + 3 1 6 8 9 + 6 1 3 4 9 + 6 1 3 5 9 +[ dihedrals ] + 3 6 1 2 4 + 1 4 3 5 4 + 1 7 6 8 4 diff --git a/tests/test_files/assets/amber14sb.ff/watermodels.dat b/tests/test_files/assets/amber14sb.ff/watermodels.dat new file mode 100644 index 0000000..420808d --- /dev/null +++ b/tests/test_files/assets/amber14sb.ff/watermodels.dat @@ -0,0 +1,5 @@ +tip3p TIP3P TIP 3-point, recommended +tip4p TIP4P TIP 4-point +tip4pew TIP4P-Ew TIP 4-point optimized with Ewald +spc SPC simple point charge +spce SPC/E extended simple point charge diff --git a/tests/test_files/test_topology/amber14sb.ff b/tests/test_files/test_topology/amber14sb.ff new file mode 120000 index 0000000..17546dc --- /dev/null +++ b/tests/test_files/test_topology/amber14sb.ff @@ -0,0 +1 @@ +../assets/amber14sb.ff \ No newline at end of file diff --git a/tests/test_files/test_topology/baz.top b/tests/test_files/test_topology/baz.top new file mode 100644 index 0000000..cee75c3 --- /dev/null +++ b/tests/test_files/test_topology/baz.top @@ -0,0 +1,237 @@ +; +; File 'baz.top' was generated +; By user: edme (57293) +; On host: otter01 +; At date: Thu Dec 4 20:04:14 2025 +; +; This is a standalone topology file +; +; Created by: +; :-) GROMACS - gmx pdb2gmx, 2024.6 (-: +; +; Executable: /mpcdf/soft/SLE_15/packages/znver4/gromacs/gcc_14-14.1.0-cuda_12.8-12.8.1-openmpi_5.0-5.0.8/2024.6/bin/gmx +; Data prefix: /mpcdf/soft/SLE_15/packages/znver4/gromacs/gcc_14-14.1.0-cuda_12.8-12.8.1-openmpi_5.0-5.0.8/2024.6 +; Working dir: /otter/u/edme/simulations/BAZ/BAZ_al +; Command line: +; gmx pdb2gmx -f BAZ_al.pdb -o BAZ_al.gro -p BAZ_al.top -water tip3p -ff amber14sb -ignh -nov -ter +; Force field was read from current directory or a relative path - path added. +; + +; Include forcefield parameters +#include "./amber14sb.ff/forcefield.itp" + +[ moleculetype ] +; Name nrexcl +Protein 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 ACE rtp ACE q 0.0 + 1 CT 1 ACE CH3 1 -0.3662 12.01 + 2 HC 1 ACE HH31 2 0.1123 1.008 + 3 HC 1 ACE HH32 3 0.1123 1.008 + 4 HC 1 ACE HH33 4 0.1123 1.008 + 5 C 1 ACE C 5 0.5972 12.01 + 6 O 1 ACE O 6 -0.5679 16 ; qtot 0 +; residue 2 ALA rtp ALA q 0.0 + 7 N 2 ALA N 7 -0.4157 14.01 + 8 H 2 ALA H 8 0.2719 1.008 + 9 CX 2 ALA CA 9 0.0337 12.01 + 10 H1 2 ALA HA 10 0.0823 1.008 + 11 CT 2 ALA CB 11 -0.1825 12.01 + 12 HC 2 ALA HB1 12 0.0603 1.008 + 13 HC 2 ALA HB2 13 0.0603 1.008 + 14 HC 2 ALA HB3 14 0.0603 1.008 + 15 C 2 ALA C 15 0.5973 12.01 + 16 O 2 ALA O 16 -0.5679 16 ; qtot 0 +; residue 3 NME rtp NME q 0.0 + 17 N 3 NME N 17 -0.4157 14.01 + 18 H 3 NME H 18 0.2719 1.008 + 19 CT 3 NME CH3 19 -0.149 12.01 + 20 H1 3 NME HH31 20 0.0976 1.008 + 21 H1 3 NME HH32 21 0.0976 1.008 + 22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 7 8 1 + 7 9 1 + 9 10 1 + 9 11 1 + 9 15 1 + 11 12 1 + 11 13 1 + 11 14 1 + 15 16 1 + 15 17 1 + 17 18 1 + 17 19 1 + 19 20 1 + 19 21 1 + 19 22 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 8 1 + 1 9 1 + 2 6 1 + 2 7 1 + 3 6 1 + 3 7 1 + 4 6 1 + 4 7 1 + 5 10 1 + 5 11 1 + 5 15 1 + 6 8 1 + 6 9 1 + 7 12 1 + 7 13 1 + 7 14 1 + 7 16 1 + 7 17 1 + 8 10 1 + 8 11 1 + 8 15 1 + 9 18 1 + 9 19 1 + 10 12 1 + 10 13 1 + 10 14 1 + 10 16 1 + 10 17 1 + 11 16 1 + 11 17 1 + 12 15 1 + 13 15 1 + 14 15 1 + 15 20 1 + 15 21 1 + 15 22 1 + 16 18 1 + 16 19 1 + 18 20 1 + 18 21 1 + 18 22 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 2 1 3 1 + 2 1 4 1 + 2 1 5 1 + 3 1 4 1 + 3 1 5 1 + 4 1 5 1 + 1 5 6 1 + 1 5 7 1 + 6 5 7 1 + 5 7 8 1 + 5 7 9 1 + 8 7 9 1 + 7 9 10 1 + 7 9 11 1 + 7 9 15 1 + 10 9 11 1 + 10 9 15 1 + 11 9 15 1 + 9 11 12 1 + 9 11 13 1 + 9 11 14 1 + 12 11 13 1 + 12 11 14 1 + 13 11 14 1 + 9 15 16 1 + 9 15 17 1 + 16 15 17 1 + 15 17 18 1 + 15 17 19 1 + 18 17 19 1 + 17 19 20 1 + 17 19 21 1 + 17 19 22 1 + 20 19 21 1 + 20 19 22 1 + 21 19 22 1 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 2 1 5 6 9 + 2 1 5 7 9 + 3 1 5 6 9 + 3 1 5 7 9 + 4 1 5 6 9 + 4 1 5 7 9 + 1 5 7 8 9 + 1 5 7 9 9 + 6 5 7 8 9 + 6 5 7 9 9 + 5 7 9 10 9 + 5 7 9 11 9 + 5 7 9 15 9 + 8 7 9 10 9 + 8 7 9 11 9 + 8 7 9 15 9 + 7 9 11 12 9 + 7 9 11 13 9 + 7 9 11 14 9 + 10 9 11 12 9 + 10 9 11 13 9 + 10 9 11 14 9 + 15 9 11 12 9 + 15 9 11 13 9 + 15 9 11 14 9 + 7 9 15 16 9 + 7 9 15 17 9 + 10 9 15 16 9 + 10 9 15 17 9 + 11 9 15 16 9 + 11 9 15 17 9 + 9 15 17 18 9 + 9 15 17 19 9 + 16 15 17 18 9 + 16 15 17 19 9 + 15 17 19 20 9 + 15 17 19 21 9 + 15 17 19 22 9 + 18 17 19 20 9 + 18 17 19 21 9 + 18 17 19 22 9 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 + 1 7 5 6 4 + 5 9 7 8 4 + 9 17 15 16 4 + 15 19 17 18 4 + +; Include Position restraint file +#ifdef POSRES +#include "posre.itp" +#endif + +; Include water topology +#include "./amber14sb.ff/tip3p.itp" + +#ifdef POSRES_WATER +; Position restraint for each water oxygen +[ position_restraints ] +; i funct fcx fcy fcz + 1 1 1000 1000 1000 +#endif + +; Include topology for ions +#include "./amber14sb.ff/ions.itp" + +[ system ] +; Name +Protein + +[ molecules ] +; Compound #mols +Protein 1 From 3abef75bf5041013dbdb2779a615168686fbd818 Mon Sep 17 00:00:00 2001 From: emerbitz <78315455+emerbitz@users.noreply.github.com> Date: Fri, 19 Dec 2025 21:10:13 +0100 Subject: [PATCH 4/4] increase version to 0.0.2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index beb8e9e..1d2b55a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "gmxtop" -version = "0.0.1" +version = "0.0.2" description = "Read and write GROMACS topology files and alter associated force fields parameters." license-files = ["LICEN[CS]E*"] authors = [{ name = "graeter-group"}]