VMD-L Mailing List

From: Pavan Ghatty (pavan.vmd_at_gmail.com)
Date: Mon Oct 19 2009 - 10:55:24 CDT

1000K? Are you sure this is correct?
Assuming this is the temperature you really want, I suggest you load them on
VMD, identify the name/number of the residues that are disulphide bonded and
select them in the graphical representations
(VMD->Graphics->Representations).
Hope this helps.
Pavan

On Tue, Oct 13, 2009 at 2:02 AM, Andres Morales N <
andresmoralesn2_at_hotmail.com> wrote:

>
>
>
> Dear VMD users:
>
>
> I am studing conformations of a protein that has three disulfide 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 analyse structures that were produced during the simulation. I need
> to identify if disulfide 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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