[gmx-users] GMXLIB for pdb2gmx

[Justin Lemkul]

On 11/19/19 6:55 PM, Ling Chan wrote:
> 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?

As described in that Redmine issue, you cannot override $GMXLIB, you can 
only append to it. If you wish to use modified versions of different 
force fields, you should copy that force field directory into the 
working directory and rename it, e.g. amber99.ff becomes amber99_mod.ff, 
etc.

> 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?

Only one file is read. pdb2gmx will look in the working directory first, 
then $GMXLIB, and will use the first one that it finds.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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