Re: regarding topology file generation

From: Chris Harrison (
Date: Wed Mar 04 2009 - 11:25:53 CST

It is a bit dated, but perhaps you should review the NAMD "Parameterizing a
Novel Residue" tutorial as a starting point to constructing your residue:


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Tue, Mar 3, 2009 at 4:55 AM, prasun kumar <> wrote:
> Respected all
> I am trying to make a topology file for a dimethylated lysine.For this is I
> am just modifying the lysine part available in the topology file(charmm),but
> I am not gettin the right structure
> 2nd method I have used is as following:
> generate the gromacs topology file from PRODRG server and then convert it
> into the charmm topology file with certain modifications in bond angle,again
> problem here is that I dont know the function used for the calculation of
> dihedral parameters in Gromacs.............
> 3rd method
> I got that one can generate the topology file using GENRTF(it seems to be
> the better way)
> can any one tell me how to use genrtf (although it is given there on its
> site link:
> from where I can download this software,they are telling that its included
> in charmm homepage,but i dint get where it is....................
> looking forward for a suggestions
> thanx in advance

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:26 CST