[AMBER] how to compute the protein interaction surface with the ligand

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Sat, 9 May 2020 00:57:39 +0200


I have thousands of PDB files like the attached one and want to calculate
the surface of the protein atoms that interact with the ligand. I use the
"molsurf" command in cpptraj with the following input:

parm sample.pdb
trajin sample.pdb
reference sample.pdb parm sample.pdb
mask ':LIG<:3.5 &! :LIG' maskout selection.txt maskpdb selection.pdb
molsurf intersurf1 ':LIG<:3.5 &! :LIG' out inter_surf.txt radii parse
molsurf intersurf2 ':LIG<:3.5' out inter_surf.txt radii parse
molsurf intersurf3 ':LIG<:3.5 | :LIG' out inter_surf.txt radii parse

With "mask" I want to check that the selection is correct, which is true.
However, the numbers look like this:

#Frame intersurf1 intersurf2 intersurf3
       1 1815.3845 1615.5031 1615.5031

It seems that the selection including the ligand has a smaller surface than
the selection without the ligand (fewer atoms). I guess the reason is that
the ligand occludes the pocket thus the protein atoms that interact with it
are no more accessible to the solvent. Is this the right way to compute the
protein interaction surface with the ligand, and if not, how should it be?
Should I strip the ligand from the trajectory first?

Thanks in advance.

Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic
email: tevang3.gmail.com, Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
website: https://sites.google.com/site/thomasevangelidishomepage/

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Received on Fri May 08 2020 - 16:00:02 PDT
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