Hi there. error for gmx.pdb2gmx()

[Shibo Li]

I have Gromacs 2022, and I pip install GromacsWrapper.
When I tried to script the following code, it showed me the error:

Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:56:21)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import gromacs
gromacs.pdb2gmx(f='1IEE.pdb', o='protein.gro', p='topo1.top', ff='oplssa', water='tip4p')
:-) GROMACS - gmx pdb2gmx, 2022.2 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/md
Command line:
gmx pdb2gmx -f 1IEE.pdb -o protein.gro -p topo1.top -ff oplssa -water tip4p

---

Program: gmx pdb2gmx, version 2022.2
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 227)
Function: void choose_ff_impl(const char*, char*, int, char*, int, const gmx::MDLogger&)

Inconsistency in user input:
Could not find force field 'oplssa' in current directory, install tree or
GMXLIB path.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Traceback (most recent call last):
File "", line 1, in
File "/root/miniconda3/envs/DevEnv1/lib/python3.9/site-packages/gromacs/core.py", line 398, in call
return self.run(args, **kwargs)
File "/root/miniconda3/envs/DevEnv1/lib/python3.9/site-packages/gromacs/core.py", line 178, in run
results, p = self._run_command(_args, **_kwargs)
File "/root/miniconda3/envs/DevEnv1/lib/python3.9/site-packages/gromacs/core.py", line 611, in _run_command
self.check_failure(result, command_string=p.command_string)
File "/root/miniconda3/envs/DevEnv1/lib/python3.9/site-packages/gromacs/core.py", line 566, in check_failure
raise GromacsError(rc, msg)
gromacs.exceptions.GromacsError: [Errno 1] Gromacs tool failed
Command invocation: gmx pdb2gmx -f 1IEE.pdb -o protein.gro -p topo1.top -ff oplssa -water tip4p

Dose it mean I need to config some env-setting like GMXLIB path on bashrc?

[Oliver Beckstein]

Normally, pdb2gmx should find your force field just as if you invoked it from the command line.

Does the following

gmx pdb2gmx -f 1IEE.pdb -o protein.gro -p topo1.top -ff oplssa -water tip4p

work, i.e., running the command manually?

If not, then you probably need to source your GMXRC file or do something else so that GROMACS finds what it needs.

Once you get gmx pdb2gmx to run successfully, try it through GromacsWrapper again.