[gmx-users] Handling modified residue
Dear all, I have been a GROMACS user for some time but this is my first time to handle a modified residue with an additional chemical group linked to the side chain. I do not have the permission to change/add the topology file in the system directory where GROMACS package is located. I am wondering if there is any other way to force pdbgmx to read residue topo file from specified location or other tricks I can play. Thanks for your help! Best regards, Jiang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Handling modified residue
you could try to write your top files in the working directory and use pdb2gmx -ff option. By default, gromacs first searches in the working directory. amit On Sat, Nov 14, 2009 at 9:05 AM, Jiang Zhu zhujiang2...@gmail.com wrote: Dear all, I have been a GROMACS user for some time but this is my first time to handle a modified residue with an additional chemical group linked to the side chain. I do not have the permission to change/add the topology file in the system directory where GROMACS package is located. I am wondering if there is any other way to force pdbgmx to read residue topo file from specified location or other tricks I can play. Thanks for your help! Best regards, Jiang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Handling modified residue
Jiang, pdb2gmx first looks for files in your working directory, and then in gromacs directory. Hope this helps, Rui Rodrigues On Sat, 14 Nov 2009 12:05:04 -0500, Jiang Zhu wrote Dear all, I have been a GROMACS user for some time but this is my first time to handle a modified residue with an additional chemical group linked to the side chain. I do not have the permission to change/add the topology file in the system directory where GROMACS package is located. I am wondering if there is any other way to force pdbgmx to read residue topo file from specified location or other tricks I can play. Thanks for your help! Best regards, Jiang -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
