[AMBER] how to identify lipids around a protein

From: Sally Pias <sallypias.gmail.com>
Date: Fri, 29 May 2020 18:53:48 -0600

Dear all,

I am in search of a strategy to determine lipids in contact with a
transmembrane protein and, ideally, in layers beyond the immediate
protein-lipid interface. The primary goal is to analyze the dynamics of the
lipids near the protein, to determine whether they are dampened relative to
the rest of the lipids in the bilayer. I would appreciate suggestions (1)
on how to identify the bordering lipid residues - e.g., something like the
cpptraj "closest" command, and (2) on how to analyze the lipid tail
dynamics - especially to determine whether trans-gauche isomerization is
slower for the bordering lipids.

Thanks very much,

Sally Pias
Department of Chemistry
New Mexico Tech
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Received on Fri May 29 2020 - 18:00:02 PDT
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