Just an update to this thread:
Thanks to instruction by Dr. Ray Luo, I noticed that the
"_MMPBSA_complex_pb" file ends with this message:
"PB Bomb in pb_aaradi(): No radius assigned for atom 29 CA XC"
I checked the residue 29 in the complex prmtop with parmed and realized
that the CA atom had all parameters. So I added "radiopt=0, " to the &pb
namelist to tell sander to read the radii from the prmtop file, and the
problem is solved.
Hamed S. Hayatshahi
>
>
> Date: Thu, 1 Oct 2020 20:16:16 -0700
> From: Ray Luo <rluo.uci.edu>
> Subject: Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is
> required, not 'str'
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAOg1T6QjHcjxuZW9eF1ZoLV_FJiQ_vVM7NPbO6jHtwiz142_6w.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hamed,
>
> Do you see any output files in the working folder? It'd be nice to see
> the sander output files to know what's going on. If possible, you can
> email the files to me directly.
>
> 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 Thu, Oct 1, 2020 at 1:54 PM ?Hamed S. Hayatshahi (??? ???? ?????
> ????????)?? <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*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * 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*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * 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:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *&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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Oct 05 2020 - 11:30:02 PDT
