Thanks!!!!!!!
________________________________
From: Preeti Pandey <preetipandey2806.gmail.com>
Sent: Friday, April 17, 2020 1:43 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
Hi Eugene,
Please add the flag "-eo energy.csv", it will serve the purpose.
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 -eo energy.csv
On Fri, Apr 17, 2020 at 10:10 AM <Eugene.Billiot.tamucc.edu> wrote:
> 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?
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Regards *
*PREETI PANDEY (Ph. D.)*
-
-
-
-
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*101 Stephenson ParkwayNorman, OK 73019-5251, USA*
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Received on Fri Apr 17 2020 - 12:00:03 PDT
