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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 [email protected] | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
