GROMACS version: 2024.5
GROMACS modification: No
I have installed gromacs from source. System Debian 12. When I tried to use martini force field from the current working directory using -ff martini3.ff the pdb2gmx doesn’t read and throwing the following error:
Command line:
gmx pdb2gmx -f dmpc_bi.pdb -o dmpc_bi.gro -p dmpc_bi.top -ignh -ff martini3.ff
Program: gmx pdb2gmx, version 2024.5
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 215)
Function: std::filesystem::__cxx11::path choose_ff_impl(const char*, char*, int, const gmx::MDLogger&)
Inconsistency in user input:
Could not find force field ‘martini3.ff’ in current directory, install tree or
GMXLIB path.
For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2025.0 documentation
martini3.ff directory is present in the working directory and the contents are as follows:
~~> ls -l martini3.ff 130
total 16M
-rw-r–r-- 1 russellb russellb 0 Feb 24 18:45 forcefield.doc
-rw-r–r-- 1 russellb russellb 0 Feb 24 18:45 forcefield.itp
-rw-r–r-- 1 russellb russellb 7.7K Feb 24 18:13 martini3_ions.itp
-rw-r–r-- 1 russellb russellb 16M Feb 24 18:13 martini3.itp
-rw-r–r-- 1 russellb russellb 5.6K Feb 24 18:13 martini3_lipids.itp
drwxr-xr-x 4 russellb russellb 4.0K Feb 24 18:13 martini3_proteins/
-rw-r–r-- 1 russellb russellb 9.7K Feb 24 18:13 martini3_small_mols.itp
-rw-r----- 1 russellb russellb 15K Feb 24 18:13 martini3_sol.itp
-rw-r–r-- 1 russellb russellb 909 Feb 24 18:13 martini3_sug.itp
-rw-r----- 1 russellb russellb 15K Feb 24 18:41 martini.itp
-rw-r–r-- 1 russellb russellb 203K Feb 24 18:13 martini_v3.0.0_phospholipids_v1.it
forcefield.doc and forcefield.itp` are the two directories that I created without any contents though. I am a newbie. Could someone shed some light on this issue?
I have tried setting GMXLIB path and exported it but in vein. Any help is much appreciated.