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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 14 2023 - 04:30:02 PST
