[gmx-users] membrane protein simulation

[Diane Fournier]

Hi gmx-users

I am trying to set up an ED experiment with the low resolution structure of a membrane protein in the hope of generating NMR-like structures. >From what I have read until now, I know that I should either restrain the transmembrane domain of the enzyme (or simulate without it), or do the simulation within a bilayer membrane. The choice is somewhat complicated by the fact that the active site of the protein (which is of interest to me) is quite close to the transmembrane domain. So I think it would be safer to simulate with the membrane, or is there a simpler solution ?

Also, I am quite new to membrane protein simulation and I would like to know how the bilayer type is chosen ? (My protein is a eukaryotic enzyme naturally bound to the endoplasmic reticulum).

Any help will be apreciated.

Diane
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