VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Jul 26 2008 - 20:21:14 CDT

Assuming no one has done it before, you'd need to create a patch in
the topology file by analogy to the DISU one. It should be pretty
straightforward, at least to a first order approximation (adjusting
things like charges though should be done with care). You might also
have to define a bond and angle in the parameter file if they don't
already exist for those atom types.

The appendix of the NAMD tutorial and the Topology File and
Parameterizing a Novel Residue Tutorials might be helpful as well.
http://www.ks.uiuc.edu/Training/Tutorials/

On Jul 26, 2008, at 5:47 PM, Roman Petrenko wrote:

> Hello all,
> have anyone ever created dityrosine links (like disulfide bonds, i.e.
> between two TYR residues)? i know that psfgen must be used, just
> hoping that someone have already done this.
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati