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

Berk Hess gmx3 at hotmail.com
Fri Jan 29 10:46:24 CET 2010


I think that what you are referring to is something different.
What I have added is that you can easily add rtp files, not itp files.
For many force fields it is actually much simpler and less work to write rtp files than itp files.
So the things I have implemented might help. But they would not if you can only
generate itp files.

If you only have an itp file, you would need to strip the molecule out of the pdb beforehand,
or pdb2gmx should know how to like a certain residue type (?) to an existing itp file.


From: alanwilter at gmail.com
Date: Fri, 29 Jan 2010 09:40:20 +0000
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: including a custom itp file in topology

Hi Berk,
If pdb2gmx will do what you said below, then for me the feature is delivered.
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>


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.


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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