From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Tue Oct 13 2009 - 01:12:23 CDT

if the system is set up properly, disulfide bonds will not break:
the potential for a bond is harmonic.

btw, 1000K for a protein for 10ns is a bit harsh, isn't it?
just out of curiosity, how much of the initial secondary structure is
still there after 10ns?

eddi

On Oct 13, 2009, at 1:00 AM, Andres Morales N wrote:

>
>
> Dear VMD users:
>
>
> I am studing conformations of a protein that has three disulfude
> bonds in its native state, I equilibrate the system (protein plus
> explicit water) at 1000 K during 10 ns using molecular dynamic
> simulation with NAMD. Now I want to analize structures that were
> produced during the simulation. I need to identify if disulfude
> bonds have been broken o not. Does anybody know how can I do that?
> Are there any script to do it?
>
>
> Thanks for your suggestion
>
>
> Andres
>
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=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================