[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

[Christopher Neale]

Hello,

I have downloaded the charmm36.ff directory and would like to use it with pdb2gmx. Everything works fine if I put it in the current directory or the share/gromacs/top directory of the binary that I am using. However, I'd like to be able to put the charmm36.ff directory in an arbitrary place.

I tried setting GMXLIB, no luck. I also tried setting GMXDATA and also, separately, creating a directory structure share/gromacs/top/charm36ff and then setting GMXDATA to share/ (which seems absurdly convoluted, but is implied that it should work by the description of GMXDATA here http://www.gromacs.org/Documentation/Terminology/Environment_Variables and the text at the output of pdb2gmx:

Fatal error:
Could not find force field 'charmm36' in current directory, install tree or GMXDATA path.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I can get around this by making a link in the current directory and then using sed to change the directory structure in the resulting .top file, after which I can remove the link in the .top file.

Thank you for any advice,
Chris.