Hi,
I have a system with two ligands bound. I have prepared the system (ensureing TER records between each ligand). And this worked:
wk_prepare_receptor.py -i protein.pdb -o protein_prepared --pdb --amber_pdbqt --lib NAD.lib 521.lib --frcmod NAD.frcmod 521.frcmod
INFO:WaterKit receptor preparation:Amber lib parameter files for residue(s): NAD, LIG
INFO:WaterKit receptor preparation:Removed all hydrogen atoms
INFO:WaterKit receptor preparation:Removed all water molecules
INFO:WaterKit receptor preparation:Histidine protonation states were automatically set to: HIE - 69, HIE - 82, HIE - 138, HIE - 158, HIE - 214, HIE - 219, HIE - 232, HIE - 243, HIE - 280
However, when I try to run waterkit - it throws an error about autogrid:
run_waterkit.py -i protein_prepared_amber.pdbqt -c -21.854 -11.377 -3.436 -s 20 20 20 -n 10000 -j 16 -o traj --autogrid_exec_path /Users/michaelcarter/DD_tools/waterkit/autodocksuite-4.2.6-src/autogrid/auto/autogrid4
Traceback (most recent call last):
File "/Users/michaelcarter/miniconda3/envs/waterkit/bin/run_waterkit.py", line 7, in <module>
exec(compile(f.read(), __file__, 'exec'))
File "/Users/michaelcarter/DD_tools/waterkit/scripts/run_waterkit.py", line 102, in <module>
main()
File "/Users/michaelcarter/DD_tools/waterkit/scripts/run_waterkit.py", line 91, in main
ad_map.add_map('SW', sw_map._maps['SW'])
AttributeError: 'NoneType' object has no attribute 'add_map'
Running with only one ligand works fine for this system.
Do you have any ideas how to resolve this?
Best,
Mike
Hi,
I have a system with two ligands bound. I have prepared the system (ensureing TER records between each ligand). And this worked:
wk_prepare_receptor.py -i protein.pdb -o protein_prepared --pdb --amber_pdbqt --lib NAD.lib 521.lib --frcmod NAD.frcmod 521.frcmodHowever, when I try to run waterkit - it throws an error about autogrid:
run_waterkit.py -i protein_prepared_amber.pdbqt -c -21.854 -11.377 -3.436 -s 20 20 20 -n 10000 -j 16 -o traj --autogrid_exec_path /Users/michaelcarter/DD_tools/waterkit/autodocksuite-4.2.6-src/autogrid/auto/autogrid4Running with only one ligand works fine for this system.
Do you have any ideas how to resolve this?
Best,
Mike