modified residues cause problems in automatic restraint generation

[cbergonzo]

When using AmberMdPrep.sh to relax a system with modified residues, the program does not count the modified residues as part of the restrained set. Instead, the program increments the number of unmodified residues (N), and sets that as the total number of restrained residues from :1-N, irrespective of where modifications are included. For example, if I have a sequence that is AAAXGGG, the restraints will include :1-6, even though residue 4 is modified and residue 7 is not. I have tested this with modxna tutorial section 3.2 topology and restart files (1nao), which result in the following restraintmasks:

step1.in: ntr = 1, restraintmask = ":1-13&!@h=", restraint_wt = 5.0,
step2.in: ntr = 1, restraintmask = ":1-13&!@h=", restraint_wt = 5.0,
step3.in: ntr = 1, restraintmask = ":1-13&!@h=", restraint_wt = 2.0,
step4.in: ntr = 1, restraintmask = ":1-13&!@h=", restraint_wt = 0.1,
step6.in: ntr = 1, restraintmask = ":1-13&!@h=", restraint_wt = 1.0,
step7.in: ntr = 1, restraintmask = ":1-13&!@h=", restraint_wt = 0.5,
step8.in: ntr = 1, restraintmask = ":1-13@P,O5',C5',C4',C3',O3'", restraint_wt = 0.5,

Sequence
5'GGA GAU GAC 3' 5'(5MG)-(OMU)-(OMC)-ATCT-(OMC)-(3MC)3'
=13 unmodified nucleotides and 5 modified nucleotides

[drroe]

I can reproduce the issue. I'll work on a fix. Thanks for the report!

[drroe]

Should be addressed by #11.