From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Fri Feb 29 2008 - 15:01:10 CST

I use Gromos 53A6 force-field and initially everything is fine.

-----Original Message-----
From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
Date: Fri, 29 Feb 2008 14:47:55 -0500 (EST)
Subject: Re: vmd-l: unusual bond between the cysteine and arginine residue during the simulation

On Fri, 29 Feb 2008, OZGE ENGIN wrote:

OE> Hi all,
OE>

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.

axel.

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

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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If you make something idiot-proof, the universe creates a better idiot.
Ozge Engin
=================================
Computational Science & Engineering
Koc University