Re: Breaking of Disulfide Bonds

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed May 30 2012 - 23:29:16 CDT

You have to tell psfgen to create a PSF where the cysteines form a
disulfide bond. Otherwise the sulfur atom of the cysteines will be
protonated and not form a disulfide bond.

Gianluca

On Thu, 31 May 2012, Aron Broom wrote:

> during classical MD it shouldn't be possible for covalent bonds to break, so this suggests
> something is wrong with your forcefield parameters.  And what do you mean by "break"?  How
> large does the distance become?  Which forcefield are you using? 
>
> On Thu, May 31, 2012 at 12:09 AM, Kapil jain <noxtreme007_at_gmail.com> wrote:
> Hi all,
> I am running md simulation on homology model of a membrane protein, following the
> membrane protein tutorial. During the minimization and equilibriation with protein
> constrained, the disulfide bond breaks. What can be the possible cause for this or
> does it happens naturally during the minimization? Are there any means to preserve
> disulfide bond?
>
> Regards
>
> Kapil Jain
>
>
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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