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
From: alanwil...@gmail.com
Date: Fri, 29 Jan 2010 09:20:31 +0000
To: j...@drugdiscoveryathome.com
CC: gmx-users@gromacs.org; a...@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.
Cheers,Alan
On Thu, Jan 28, 2010 at 17:13, Jack Shultz <j...@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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