[gmx-users] Handling modified residue

Amit Choubey kgp.amit at gmail.com
Sat Nov 14 19:00:04 CET 2009

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


On Sat, Nov 14, 2009 at 9:05 AM, Jiang Zhu <zhujiang2005 at 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
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