VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 29 2008 - 13:58:08 CST

How "long" is it? This could be due to PBC wrapping or simply
because the atoms started near each other in the initial trajectory
frame where automatic bond determination was done, but subsequently
moved apart. It depends on how VMD got the bond information.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 29, 2008 at 09:30:01PM +0200, OZGE ENGIN wrote:
> Hi all,
>
> I perform a simulation of a 24-residue peptide at air/water interface. While I am looking at the trajectory, I see that there is an unusual bond (long bond) between the cysteine and arginine residue. However, I have another cysteine residue but it does not make any bond with any other residue.Both residues are charged.
>
> What may be the reason?
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University 

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