Re: Cyclopeptide: connectivity between the first and last residues

From: David Tanner (
Date: Mon Sep 29 2008 - 15:36:31 CDT


1) You are allowed to edit your .psf file. You'll want to look at the
two amino acids which you are trying to bind together; you can type
the bonds/angles/dihedrals into the psf file under their respective
headings (just follow the pattern you see in the psf file).

2) To figure out what bonds/angles... should exist, find those same
two amino acids in another psf file and see what
bonds/angles/dihedrals are assigned between them. If you don't have
this information, you can select the two amino acids you are trying to
connect in VMD, write them to a pdb file, and try using psfgen to
generate a psf file from it. That might show you what
bonds/angles/dihedrals you need to add.

3) Also be sure to delete from your psf file any bonds which shouldn't
have been there in the first place (due to the irregular geometry).

Thank you,
David E. Tanner

David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
(217) 244 - 2905

On Mon, Sep 29, 2008 at 12:52 PM, List <> wrote:
> Dear NAMD experts,
> I have a question around running MD for a CYCLOPEPTIDE. When the regular
> procedure was applied, after minization, the bond between the first and the
> last residues got broken. I guess these two residues are not connected in
> the .psf file although they are geometry-wise. I wonder if there is any way
> to specify the connectivity or apply any constraint, so that the first and
> last residues will remain bonded/connected throughout the MD simulation.
> Any help will be greatly appreciated,
> Shirley

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