[gmx-users] membrane protein simulation

[Justin A. Lemkul]

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
> hello users
> I am starting a membrane protein simulation. I had some missing residues in
> the protein which have been added now. Should I minimise in vaccum before
> insertion of the protein in bilayer?

Couldn't hurt, but probably not necessary.  Remember that energy minimization
simply generates a reasonable starting structure.

> Another question : Is it necessary to do simulation in water before inserting
> protein nto bilayer?

Check the literature to see what others have done and recommend.

-Justin

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========================================

Justin A. Lemkul
Graduate Research Assistant
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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