Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations

From: <Eugene.Billiot.tamucc.edu>
Date: Fri, 17 Apr 2020 15:09:42 +0000

Dr. Luo,
Thanks for your reply. Sorry for the late reply. I have been out of the office and unavailable for a bit. Anyway, I do not see any file named "energies.csv" or any csv files in my working folder. Is there a command I should add to my run that would create such a file. Below is an example of the info I used to calculate the binding energies.


mpirun -np 20 MMPBSA.py.MPI -O -i mmpbsa.in -o OOF_complex_water_PB.dat -sp OOF_complex_water.prmtop -cp COMPLEX_OOF_water.prmtop -rp RECEPTOR_OOF_water.prmtop -lp LIGAND_OOF_water.prmtop -y OOF_complex_water-new-final_60ns_10.traj

mmpbsa.in file
Input file for running PB and GB
&general
   verbose=1, entropy=0
/
&gb
  igb=2, saltcon=0.100
/
#&pb
  istrng=0.100,
/



________________________________
From: Ray Luo <
>
Sent: Sunday, April 12, 2020 9:33 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations

Eugene,

There should be an "energies.csv" file in your working folder, which
has all the info you need ...

All the best,
Ray 

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sat, Apr 11, 2020 at 7:49 AM Billiot, Eugene
<Eugene.Billiot.tamucc.edu> wrote:
>
> Hello All,
> I am using MMPBSA to calculate ligand binding energies for a variety of analytes with various amino acid based micellar systems.  I would like to be able to plot ligand binding energy as a function of simulation time.  When running MMPBSA calculations does it calculate energies for each frame and then print out an average at the end.  If so, does it create a file with the calculated PG and GB energies per frame that I can then use to plot energy calculations for each frame?  Is there any way I can examine the binding energy as a function of simulation time?
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Received on Fri Apr 17 2020 - 08:30:02 PDT
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