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

From: Daniel Roe <>
Date: Wed, 20 May 2020 12:00:42 -0400


I know I responded to some of this off-list, but I also wanted to
respond on-list so it shows up in the future for people with a similar

To be honest, 'molsurf' probably isn't a good fit for what you want
here. The 'molsurf' command isn't good for getting partial surfaces.
The 'molsurf' program that I adapted the code from didn't have a
complete per-atom surface area contribution, and I've never had the
time to implement it myself. So if you do say :1-3, it's going to give
you the *total* surface area of residues 1 to 3, not the contribution
of residues 1 to 3 as part of a larger surface area. The LCPO surface
area ('surf') will do a "partial" surface area, but that surface area
is much less accurate.

Hopefully this helps a little bit.


On Fri, May 8, 2020 at 6:58 PM Thomas Evangelidis <> wrote:
> Greetings,
> 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
> go
> 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.
> Thomas
> --
> ======================================================================
> Dr. Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
> of Sciences <>, Prague,
> Czech Republic
> &
> CEITEC - Central European Institute of Technology
> <>, Brno,
> Czech Republic
> email:, Twitter: tevangelidis
> <>, LinkedIn: Thomas Evangelidis
> <>
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Received on Wed May 20 2020 - 09:30:02 PDT
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