[gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out

Mark Abraham mark.abraham at anu.edu.au
Fri Jun 4 14:42:35 CEST 2010

----- Original Message -----
From: maria goranovic <mariagoranovic at gmail.com>
Date: Friday, June 4, 2010 18:51
Subject: [gmx-users] writing patches to combine two molecules into a dimer	and getting the combined topology out
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Dear Friends
> I am looking to make the topology of a lipid bonded to a peptide. Although this can be done by defining a new residue in the .rtp, this method may not be the best if I want to repeat the procedure for different residues on the peptide. Is it possible in gromacs to write a patch (like in CHARMM), where one could combine two molecules using some sort of patch?

Not really. The best suggestion I can make is to use http://www.gromacs.org/Documentation/File_Formats/specbond.dat. This will require an .rtp entry for the "isolated" lipid, but that's no more work than a CHARMM patch residue.

>  This is probably implemented for proteins anyway, when amino acids are polymerized. The idea is to 

That mechanism relies on knowing in advance there's a head-to-tail CO-to-NH linkage, and doesn't generalise.

> have individual topologies and coordinates of the lipid and amino acid, and writing some sort of patch to combine these two, by making new bonds, and elminating some old ones. What would be the best (not necassarily the easiest??) to do this?

The above seems best to me. If you find a good workflow, then please consider adding it to the that wiki page. This kind of question has been asked before.

> Maria G.
> Technical University of Denmark
> Copenhagen
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