Hi Sally,
Please check it out if you find it helpful. It works with different
trajectory formats.
https://github.com/prajwal07/FInd_Surrounding_Residues/blob/master/README.md
Thanks and best regards,
---------------------------------------------
Prajwal Nandekar, Ph.D. (Pharmacoinformatics)
On Sat, May 30, 2020, 6:24 AM Sally Pias <sallypias.gmail.com> wrote:
> 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
>
> Sally Pias
> Department of Chemistry
> New Mexico Tech
> sallypias.gmail.com
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Received on Fri May 29 2020 - 18:30:01 PDT
