[gmx-users] Suggestion required for calculation of membrane contact sites and Lipid binding strength

Antara mazumdar antara.mazumdar at igib.in
Sat May 28 16:40:11 CEST 2016

Dear Gromacs users,

    Can anyone suggest me a way to find the membrane contact sites i.e. the
lipids that are making contact with protein residues with respect to time
from a  membrane protein simulation? I have calculated the distance and
contact of protein residues from upper leaflet atoms of bilayer already
with a cutoff between 0.5 nm and 0.7 nm.

I have the lipid numbers in the log file from g_hbond as well as g_dist.
Should i be taking all these into account or a cutoff needs to be taken and
can this be calculated wrt time?

Secondly, has anyone found out the lipid binding strength from membrane
protein simulations? Can we call the frequency of a protein residue to make
a contact as its lipid binding strength? Here also, is there some way to
find the binding strength wrt time?

Kind Regards,

Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040

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