[gmx-users] MD simulation of protein-protein complex

[Justin Lemkul]

On 2/21/13 10:18 AM, shahid nayeem wrote:
> Dear all
> I want to simulate a protein complex with 4 chains two of which is
> linked with disulfide bonds. Does this simulation requires that all
> chains are merged into one molecule definition or I should merge only
> two chains which are linked with disulfide bonds. I want that all
> these four chains remains bonded during simulation.

The minimum requirement is that the chains involved in the disulfide be present 
in a merged [moleculetype].  How you treat the others is irrelevant.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
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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