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

Alan alanwilter at gmail.com
Fri Jan 29 10:20:31 CET 2010

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:

> Hi,
> 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?
> --
> Jack
> http://drugdiscoveryathome.com
> http://hydrogenathome.org

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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