[AMBER] using accelerated MD on membrane proteins?

From: Homeo Morphism <homeo.morphizm.gmail.com>
Date: Wed, 28 Aug 2019 19:09:15 +0300

I'm going through section 20.2.3 of the Amber manual. In there the
parameters necessary for starting aMD are calculated in terms of the number
of protein residues. I suspect that protein residues are just sort of a
placeholder for dihedrals. But what if I have non-protein residue
dihedrals? Such as lipid dihedrals, for example. How do I account for them?
Any ideas how aMD parameters should be evaluated in that case? Thank you.
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Received on Wed Aug 28 2019 - 09:30:02 PDT
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