Thank you sir for your response. But, I am observing that, when I am
introducing "scale= 0.5" parameter in mmpbsa.in, then I am getting the
error. But the same input file while running without "scale" keyword then
it is working fine.
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12/14/23,
10:18:55 PM
On Thu, Dec 14, 2023 at 5:50 PM Dr. Anselm Horn via AMBER <amber.ambermd.org>
wrote:
> Kankana,
>
> although I'm no specialist in MM/PBSA, I noticed that your input file
> contains potential formatting problems:
> - there's no separating comma between the two parameter/value pairs in
> your "general" section;
> - you commented out the start and content of the "gb" section, but not
> the closeing "/"
>
> Maybe that helps.
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 14.12.2023 um 12:56 schrieb Kankana Bhattacharjee via AMBER:
> > Dear AMBER users,
> >
> > I am doing MMPBSA calculation of a protein ligand complex. Now, after
> > executing the command, I am getting the error as:
> > My command line was:
> >
> > *MMPBSA.py -i mmpbsa.in <http://mmpbsa.in> -o FINAL_RESULTS_MMPBSA.dat
> -sp
> > prot.top -cp com.top -rp rec.top -lp lig.top -y traj.crd -eo energy.dat*
> > File "/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/MMPBSA.py", line
> > 100, in <module>
> > app.run_mmpbsa()
> > File
> >
> "/apps/scratch/compile/amber22/amber22_cpu_mpi/lib/python3.9/site-packages/MMPBSA_mods/main.py",
> > line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> >
> "/apps/scratch/compile/amber22/amber22_cpu_mpi/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
> > line 82, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> >
> "/apps/scratch/compile/amber22/amber22_cpu_mpi/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
> > line 428, in run
> > error_list = [s.strip() for s in out.split('\n')
> > TypeError: a bytes-like object is required, not 's
> >
> > I am also attaching the MMPBSA.in file.
> >
> > I am not able to figure out the error.
> > Please provide me some suggestions.
> >
> > Thanks & Regards
> > Kankana Bhattacharjee
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Thu Dec 14 2023 - 09:00:02 PST
