----- Original Message ----- From: maria goranovic <mariagorano...@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@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. Mark > Maria G. > Technical University of Denmark > Copenhagen > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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