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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 Thu, Oct 1, 2020 at 1:54 PM Hamed S. Hayatshahi (سید حامد سادات
حیاتشاهی) <sh.sadat.gmail.com> wrote:
>
> Dear Amber community,
>
> I am using MMPBSA.py of AmberTools20 to calculate the binding energy in a
> protein-ligand system. I get the following error:
>
> *Beginning PB calculations with /home/chem/AmberTools20/amber20/bin/sander*
>
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> * calculating complex contribution... File
> "/home/chem/AmberTools20/amber20/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa() File
> "/home/chem/AmberTools20/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File
> "/home/chem/AmberTools20/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run calc.run(rank, stdout=stdout, stderr=stderr) File
> "/home/chem/AmberTools20/amber20/lib/python3.8/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
> 'str'Exiting. All files have been retained.*
>
> For the same system and the same topology files, I get the same error with
> AmberTools20 on two machines with Ubuntu and Centos. I get the the
> following similar error with AmberTools18 on a different machine:
>
> *Beginning PB calculations with
> /cm/shared/apps/scientific/AMBER/amber18/bin/sander*
>
>
>
>
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>
>
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>
>
> * calculating complex contribution... File
> "/cm/shared/apps/scientific/AMBER/amber18/bin/MMPBSA.py", line 100, in
> <module> app.run_mmpbsa() File
> "/cm/shared/apps/scientific/AMBER/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File
> "/cm/shared/apps/scientific/AMBER/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run calc.run(rank, stdout=stdout, stderr=stderr) File
> "/cm/shared/apps/scientific/AMBER/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 433, in run self.prmtop) + '\n\t'.join(error_list) +
> '\n')CalcError: /cm/shared/apps/scientific/AMBER/amber18/bin/sander failed
> with prmtop ../complex.parm7!*
> Here is my mmpbsa.in script:
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> *&general startframe=1, endframe=5, interval=1,
> receptor_mask=":1-130", ligand_mask=":131", strip_mask="@2121-56249",
> verbose=1, keep_files=1, netcdf=1,/&pb istrng=0.15, /&decomp
> idecomp=1, print_res="36,131", dec_verbose=1,/*
>
> I run it with:
>
> MMPBSA.py -O -i mmpbsa.in -o mmpbsa.out -do decomp.csv -sp full.parm7 -cp
> complex.parm7 -rp rec.parm7 -lp lig.parm7 -y traj_1.nc
>
> I prepared the prmtop files with:
>
> ante-MMPBSA.py -p full.parm7 -r rec.parm7 -l lig.parm7 -c complex.parm7 -s
> .2121-56249 -m :1-130 --radii mbondi2
>
> I checked all parm7 files that I used above and the number of atoms match
> with what I expect as ligand, receptor, complex and colvated systems.
>
> I found a similar thread from 2018 in which a similar problem has been
> reported but found no answer for it:
>
> http://archive.ambermd.org/201804/0329.html
>
> Other system details: Protein with 130 residues and a negatively-charged
> ligand with 78 atoms. Total of 56249 atoms including OPC water, and ions in
> the solvated system.
>
> Could you please help me figure out the problem with this calculation?
>
> Thanks,
> Hamed S. Hayatshahi
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Received on Thu Oct 01 2020 - 20:30:02 PDT