[gmx-users] Re: including a custom itp file in topology

Alan alanwilter at gmail.com
Fri Jan 29 10:40:20 CET 2010

Hi Berk,

If pdb2gmx will do what you said below, then for me the feature is

To be sure, what I would like to have (and I guess Jack too) is:

- one has a pdb with protetin + ligands (one or more)
- have the topologies itp files for the ligands already created
- run pdb2gmx on complex.pdb and have pdb2gmx to *know* about the ligands
and generated the respective top and gro files ready for EM and MD.

It is that what I understood Jack wants and what you said you have added to
the coming pdb2gmx (for gmx 4.1?).

Many thanks,


On Fri, Jan 29, 2010 at 09:28, <gmx-users-request at gromacs.org> wrote:
>  From: Berk Hess <gmx3 at hotmail.com>
> Hi,
> I don't understand exactly what is the requested feature here.
> I am currently reorganizing the force field setup in Gromacs to more
> cleanly support AMBER and CHARMM
> and adding some extra functionality. I started a discussion on the
> gmx-developers list on this topic.
> On feature I have added is that rtp, hdb, etc files no longer have fixed
> names and you can have multiple
> of them. So you can just put, e.g., a file called ligand.itp in your force
> field or current dir and pdb2gmx
> will read it.
> Berk

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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