Closed lichman0405 closed 2 years ago
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.
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.
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?