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

Mark Abraham mark.abraham at anu.edu.au
Fri Jan 29 02:46:02 CET 2010

----- Original Message -----
From: Jack Shultz <js at drugdiscoveryathome.com>
Date: Friday, January 29, 2010 4:15
Subject: [gmx-users] including a custom itp file in topology
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: Alan <alanwilter at gmail.com>, Andrey Voronkov <av at drugdiscoveryathome.com>

> 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?

The procedure looks good, but there's no way to get pdb2gmx to do this step for you. It will be straightforward to use sed or perl to add the #include and the [molecules] changes into the .top produced by pdb2gmx - that's what these tools are for!


head -n -2 topol.top > new.top
echo '#include "ligand.itp"' >> new.top
tail -n 2 topol.top > footer >> new.top
echo 'ligand 1' >> new.top

will do the job if the last two lines of topol.top are of the form

Protein 1

This kind of UNIX-tool scripted problem-solving using head, tail, cut, paste, grep, sed, uniq, sort, echo, perl, cat and others often requires some consultation of the man pages and awareness that the tool exists... but most problems you want to solve have been solved before and the tool is out there already... Google away!


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