Dear all,
I am interested in carrying out per residue free energy decomposition for a
protein - ligand complex.
The residue code of my ligand is 671.
a) Is there a way to specify in the command (mmpbsa.in file) to run
decomposition analysis of the residues that are 4 angstroms around the
ligand?
b) Would it take the same time to decompose the values for all the
residues?
c) Is there a way to incorporate these values into a pdb file for
visualization? For example,
mmpbsa_perresidue.png
<
https://drive.google.com/a/sssihl.edu.in/file/d/11SMwbtrJ31xyqxINqACEujqmmXozY2zo/view?usp=drive_web>
d) I had neutralized the system with counter ions and did not saturate the
system with any more salt. would this script look correct for mmpbsa, in
this case?
----
Input file for running PB and GB
&general
endframe=50, verbose=2,
keep_files=1,
full_traj=1,
netcdf=1,
entropy=0,
/
&gb
igb=5,
/
&pb
inp=1,
radiopt=0,
/
-----
Thank you in advance.
--
Regards,
Prasanth.
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Received on Thu May 21 2020 - 05:00:02 PDT
