From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed May 30 2012 - 23:29:53 CDT
You need to build it into your topology in the first place. See the "PRES DISU" patch in the charmm topology file. You add patches after you generate segments but before adding coordinates with psfgen.
On May 30, 2012, at 11:09 PM, Kapil jain 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
>
>
>
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