[gmx-users] generating topology for artificial residues

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 10 20:31:56 CEST 2008

Grange Hermitage wrote:
> Hi all,
> What approach to use to generate a topology file for peptides which 
> include artificial residues such as serine with its sidechain extended 
> by two carbons to double bond with another such residue i.e.
> Also I need to generate a topology for another type of 
> artificial peptide which includes beta-3 residues (C inserted in 
> mainchain between CA and C ).
> Say I want to use a force field other than the 2 supported by the 
> PRODRG2.5 server.
> I have tried to defining ff*.rtp residue definitions, but .top generated 
> by pdb2top are missing defaults essential for grompp (gb_ gd_). The 
> residue definitions have only [ atom ] specifications, allowing 
> the other sections to default as per the manual.

Well, then the defaults don't apply for whatever you've tried to connect. 
Basically, check out the *bon.itp file for your force field and make sure the 
parameters that you think you are generating are actually there, and then check 
the naming you've given your atom types to make sure it is appropriate and 
compatible with the ones that the force field is expecting.

Without showing us what you've tried, it's difficult to diagnose.


> thanks,
>    Grange.
> ------------------------------------------------------------------------
> Start at the new Yahoo!7 for a better online experience - Start Here 
> <http://au.rd.yahoo.com/mail/taglines/au/y7mail/default/*http://au.docs.yahoo.com/somethingwonderful/index.php?p1=brand&p2=other&p3=au&p4=tagline>.
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list