[gmx-users] Re: Problem in Disulfide Bond

[Justin A. Lemkul]

parthiban at ncbs.res.in wrote:
> Hi
> 
> I am using a dimer for my simulation system which is connected by 2
> disulfide bonds.
> After energy minimization for even few cycles, the disulfide bond breaks
> which is not expected.

Bonds do not break in classical molecular mechanics.  One of two things is 
happening:

1. There was never a bond to begin with (check your topology)
2. The bond is highly strained, in which case something is wrong with your 
structure.

> i have applied amber99 force field and prepared the system. while i tried
> with another force field in Gromacs which did not worked at all.

What does that mean?  What failed?

> also i have tried by editing specbond.dat as well but of no use.

In what way?  Have you seen the information at:

http://www.gromacs.org/Documentation/File_Formats/specbond.dat

-Justin

> can any one share/discuss some ideas how to fix this.
> 
> reg's,
> Parthiban.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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