Daniel,
The results I get from PyMOL are contradictory. I want more or less to
compute the interface surface between the ligand and the protein and as I
stated in my first email, I have hundreds of thousands of them.
load sample.pdb
> select pocket, sample within 3.5 of resn LIG;
> set dot_solvent, 0;
> get_area pocket;
> set dot_solvent, 1;
> get_area pocket;
> select pocket, not resn LIG within 3.5 of resn LIG;
> set dot_solvent, 0;
> get_area pocket;
> set dot_solvent, 1;
> get_area pocket;
>
molecular surface with the ligand = 1151.064 Angstroms^2
SASA with the ligand = 132.465 Angstroms^2.
molecular surface without the ligand = 793.769 Angstroms^2
SASA without the ligand = 103.238 Angstroms^2
Now I am really confused. These numbers are far from those I got from
cpptraj. The reason I used the "molsurf" command with the "parse" radii is
- as stated in the manual - because I don't have topology files and hence
no info about GB/VDW radii. I could generate topologies, but that would be
much slower than analyzing all these PDB files with PyMOL in batch mode.
Can you please shed some light on this?
Thanks.
Thomas
On Sat, 9 May 2020 at 00:57, Thomas Evangelidis <tevang3.gmail.com> 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 <
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
<
https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
website: https://sites.google.com/site/thomasevangelidishomepage/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 18 2020 - 14:00:01 PDT
