From: Axel Kohlmeyer (
Date: Fri Feb 29 2008 - 13:47:55 CST

On Fri, 29 Feb 2008, OZGE ENGIN wrote:

OE> Hi all,

OE> I perform a simulation of a 24-residue peptide at air/water
OE> interface. While I am looking at the trajectory, I see that there is
OE> an unusual bond (long bond) between the cysteine and arginine
OE> residue. However, I have another cysteine residue but it does not
OE> make any bond with any other residue.Both residues are charged.

OE> What may be the reason?

bonds are taken from the .psf file (i assume you use NAMD
and load .psf and .dcd), so your .psf file is not correct.


OE> Ozge Engin
OE> =================================
OE> Computational Science & Engineering
OE> Koc University

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.