After installing OpenMM and all other required dependencies I started equilibrating pose0 from the default example specified in input-sdr-openmm.in. This process ran without an issue and I performed local OpenMM simulations on an RTX4090 within a couple minutes of all 9 segments.
In the next step, the fe simulation, I am running into the following issue:
(abfe) root@bd6f9c20ec44:/BAT.py/BAT# python BAT.py -i input-sdr-openmm.in -s fe
lambda values: [0.009219682876640378, 0.0479413718147626, 0.11504866290284765, 0.20634102285669126, 0.31608425050090994, 0.43738329574426554, 0.5626167042557344, 0.6839157494990901, 0.7936589771433087, 0.8849513370971523, 0.9520586281852375, 0.9907803171233596]
Gaussian weights: [0.02358766819325601, 0.05346966299765944, 0.08003916427167306, 0.10158371336153282, 0.11674626826917732, 0.12457352290670134, 0.12457352290670134, 0.11674626826917732, 0.10158371336153282, 0.08003916427167306, 0.05346966299765944, 0.02358766819325601]
['m', 'n', 'e', 'v']
sdr
[0.0, 0.1, 0.24, 0.56, 1.33, 3.16, 7.5, 17.78, 42.17, 100.0]
[0.009219682876640378, 0.0479413718147626, 0.11504866290284765, 0.20634102285669126, 0.31608425050090994, 0.43738329574426554, 0.5626167042557344, 0.6839157494990901, 0.7936589771433087, 0.8849513370971523, 0.9520586281852375, 0.9907803171233596]
4.0
0.9
Error: 'md08.dcd': No such file or directory
Error: Could not set up input trajectory 'md08.dcd'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: 'md08.dcd': No such file or directory
Error: Could not set up input trajectory 'md08.dcd'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: 'md08.dcd': No such file or directory
Error: Could not set up input trajectory 'md08.dcd'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: 'md08.dcd': No such file or directory
Error: Could not set up input trajectory 'md08.dcd'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Setting up pose0
window: t00 weight: 100.0
Traceback (most recent call last):
File "BAT.py", line 840, in <module>
anch = build.build_dec(fwin, hmr, mol, pose, comp, win, water_model, ntpr, ntwr, ntwe, ntwx, cut, gamma_ln, barostat, receptor_ff, ligand_ff, dt, sdr_dist, dec_method, l1_x, l1_y, l1_z, l1_range, min_adis, max_adis, ion_def, other_mol, solv_shell)
File "/BAT.py/BAT/lib/build.py", line 627, in build_dec
shutil.copy('../../build_files/%s.pdb' %mol.lower(), './')
File "/root/miniforge3/envs/abfe/lib/python3.7/shutil.py", line 248, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/root/miniforge3/envs/abfe/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '../../build_files/lig.pdb'
The first issue is an Error re: a missing md08.dcd files. I am running this script from the BAT subdirectory. The trajectories of the equilibrated complexes are located in equal/pose0. I double checked that all dcd files for the 9 components are there. I also moved the dcd files into /BAT2.py/BAT in order to be extra sure that there is not a path issue.
The second issue is a missing lig.pdb file in the build_files directory. When checking the github repo, I could not find such a file and I did not find a related line in the BAT2 input configuration file.
Is this an error something you have seen before with OpenMM in BAT2? I am happy to share a docker image to more easily reproduce the issue if that is helpful.