[gmx-users] membrane protein simulation

Mark Abraham mark.abraham at anu.edu.au
Wed Jan 30 12:34:09 CET 2008

> 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?

That depends how "bad" the new residue coordinates are, and whether vacuum
EM is better than the current ones. Probably the reason these residues
were missing was that you've got a starting structure from somewhere that
didn't have these residues resolved because they're disordered. You might
know this already from your background reading on this protein (hint,
hint). In such a case, so long as your bond lengths are all reasonable,
then it won't matter at all what you do before you solvate the system.
Whether their behaviour is at all relevant for the observable you wish to
study is another matter, and you need to address that yourself.

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

Err, that depends what you want to do. A protein that belongs in a bilayer
will be very unhappy in water and could do anything imaginable. Hint -
have a look at the residues that are on the "outside" of protein on the
bit that belongs in the bilayer, and another look at the residues from
some other protein part that does not belong in a lipid phase. The two
sets will be quite different. Background knowledge of protein chemistry
should have told you this... perhaps you should do some more of this to
avoid silly mistakes?


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