Re: [AMBER] MMPBSA.py bad atom type: M1 error

From: Ray Luo <rluo.uci.edu> Date: Thu, 3 Dec 2020 09:46:19 -0800

--
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, Dec 3, 2020 at 8:36 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> I'm just trying to reach out again to the expert users and developer of
> MMPBSA.
> Can someone on the list, please suggest on this atom type error in
> MMPBSA.py?
> thanks in advance and best regards.
>
>
>
> On Mon, Nov 16, 2020 at 2:53 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > Dear All,
> > I'm trying to run MMPBSA analysis on an MD trajectory of a ligand-bound
> > metalloprotein.
> > the ligand is the 1st residue in pdb given to tleap.
> > The mmpbsa input file is given below.
> >
> > I also tried using ante-MMPBSA.py and created the receptor-ligand prmtops,
> > but these are given prmtop compatibility issues shown at the end.
> >
> > I used MMPBSA with Amber12, but a lot seems to have changed since then.
> > Thus please help me figure out what key command-line usage considerations
> > I might be missing out here.
> >
> > thank you and best regards.
> >
> > mmpbsa-decomp.in
> > &general
> >   startframe=1, endframe=100, interval=5,
> >   verbose=2, keep_files=2, netcdf=1, receptor_mask=2-386,
> > strip_mask=:387-16750,
> > /
> > &gb
> >   igb=5, saltcon=0.150,
> > /
> > &pb
> >   istrng=0.15, fillratio=4.0
> > /
> > &decomp
> >   idecomp=1, print_res="56-57; 74-75; 167; 222; 225-227; 229-231; 272-273;
> > 275-277; 336; 368; 370; 372-373"
> >   dec_verbose=1,
> > /
> >
> > (base) [exx.c107739 mmpbsa-6701-tyr]$ MMPBSA.py -O -i mmpbsa-decomp.in
> > -sp ../rouf-6701-tyr-solv.prmtop -eo gb-pbsa-snapshot-Es.csv -deo
> > residue-decomp.csv -y ../rouf-6701-tyr-solv-prod300.nc -cp
> > ../rouf-6701-tyr-dry.prmtop
> > Loading and checking parameter files for compatibility...
> > /usr/local/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py:603:
> > UserWarning: receptor_mask overwritten with default
> >
> >   warnings.warn('receptor_mask overwritten with default\n')
> > sander found! Using /usr/local/amber18/bin/sander
> > cpptraj found! Using /usr/local/amber18/bin/cpptraj
> > Preparing trajectories for simulation...
> > 20 frames were processed by cpptraj for use in calculation.
> >
> > Running calculations on normal system...
> >
> > Beginning GB calculations with /usr/local/amber18/bin/sander
> >   calculating complex contribution...
> >  bad atom type: M1
> >   File "/usr/local/amber18/bin/MMPBSA.py", line 100, in <module>
> >     app.run_mmpbsa()
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
> > 218, in run_mmpbsa
> >     self.calc_list.run(rank, self.stdout)
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 82, in run
> >     calc.run(rank, stdout=stdout, stderr=stderr)
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 157, in run
> >     self.prmtop))
> > CalcError: /usr/local/amber18/bin/sander failed with prmtop
> > ../rouf-6701-tyr-dry.prmtop!
> > Exiting. All files have been retained.
> > (base) [exx.c107739 mmpbsa-6701-tyr]$
> >
> > *Error after using ante-MMPBSA and then trying to use MMPBSA.py*
> > (base) [exx.c107739 mmpbsa-6701-tyr]$ ante-MMPBSA.py -p
> > ../rouf-6701-tyr-solv.prmtop -c rouf-tyr -r rouf -l tyr -n 1
> > Creating receptor topology file by stripping 1 from
> > ../rouf-6701-tyr-solv.prmtop
> > Done creating receptor topology file!
> >
> > Creating ligand topology file by stripping !(1) from
> > ../rouf-6701-tyr-solv.prmtop
> > Done creating ligand topology file!
> >
> > (base) [exx.c107739 mmpbsa-6701-tyr]$ MMPBSA.py -O -i mmpbsa-decomp.in
> > -sp ../rouf-6701-tyr-solv.prmtop -eo gb-pbsa-snapshot-Es.csv -deo
> > residue-decomp.csv -y ../rouf-6701-tyr-solv-prod300.nc -cp rouf-tyr -lp
> > tyr
> > Loading and checking parameter files for compatibility...
> >   File "/usr/local/amber18/bin/MMPBSA.py", line 98, in <module>
> >     app.loadcheck_prmtops()
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
> > 574, in loadcheck_prmtops
> >     FILES.receptor_prmtop, FILES.ligand_prmtop)
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> > line 98, in __init__
> >     self.complex_prmtop = LoadParm(complex_prmtop)
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/amber/readparm.py",
> > line 64, in LoadParm
> >     parm = AmberFormat(parmname)
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/amber/amberformat.py",
> > line 380, in __init__
> >     self.rdparm(fname)
> >   File
> > "/usr/local/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/amber/amberformat.py",
> > line 456, in rdparm
> >     ret = _rdparm.rdparm(fname)
> > IOError: Could not open rouf-tyr for reading
> > Exiting. All files have been retained.
> > (base) [exx.c107739 mmpbsa-6701-tyr]$
> >
> >
> >
> > --
> >
> > Regards,
> >
> > Dr. Vaibhav A. Dixit,
> >
> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> >
> >
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
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