[gmx-users] GMXLIB for pdb2gmx

[Ling Chan]

Hello colleagues,

I would like to do experiments on a force field. Hence I cloned the force field files from shares/gromacs/top to a local directory, at $HOME/top. According to the manual page at http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html
I need to set the GMXLIB environment variable to point to my directory. So I did. But then pdb2gmx still goes to the original directory, at shares/gromacs/top, before visiting $GMXLIB. As a result, the force fields are all duplicated and pdb2gmx would refuse to go ahead. This is probably the same issue as discussed here. https://redmine.gromacs.org/issues/1928

So, how can I prevent Gromacs from searching the original force field directory?

On a related note, if I am to add new residues, say Glycam ones, I would need to append new lines to the file “residuetypes.dat”, at share/gromacs/top. If I have a “residuetypes.dat” both at share/gromacs/top and at $GMXLIB, will pdb2gmx read both files?

Thank you.

Regards,
Ling

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