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

Berk Hess gmx3 at hotmail.com
Fri Jan 29 10:27:54 CET 2010


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.


From: alanwilter at gmail.com
Date: Fri, 29 Jan 2010 09:20:31 +0000
To: js at drugdiscoveryathome.com
CC: gmx-users at gromacs.org; av at drugdiscoveryathome.com
Subject: [gmx-users] Re: including a custom itp file in topology

Hi Jack,
Look, if I understand well, what you want is to be able to something like tleap does for amber, where you load all the libs you need, including the ones you created for your ligand(s), and then generate the MD input files at once needing just the complexed pdb or mol2 as input.

For pdb2gmx to do the same, you would need to tweak the files ..../gromacs/top/ffamber99sb.rtp, hdb etc., which I once considered doing that for acpypi but then it would add much more complexity for no much gain.

What I hope is for the new *pdb2gmx* (gmx 4.1 maybe? or only for gmx 5.0?) to feature, among other things, this capability as you requested.

On Thu, Jan 28, 2010 at 17:13, Jack Shultz <js at drugdiscoveryathome.com> wrote:

I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx?



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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