[gmx-users] Broken protein chain.

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear users,
> 
> Has anyone done simulation with a broken crystal structure?
> I know that it can be modeled before simulating. But I just wanted
> to know whether any one had done with the crystal structure having
> breakage as such without modelling.
> 

You need an intact starting structure to create a reasonable topology and run 
any sort of simulation.  Missing termini may not be significant, but any atoms 
or residues missing within the chain have to be reconstructed.

-Justin

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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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