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

From: Ray Luo <rluo.uci.edu> Date: Thu, 3 Dec 2020 20:40:18 -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 7:56 PM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> Dear Ray,
> I got this atom type error in Amber18.
> I just mentioned the last version, Amber12, with which I had an experience
> of performing MMPBSA analysis (successfully).
> Can you please suggest a possible solution?
> thanks and best regards
>
>
> On Fri, Dec 4, 2020 at 2:47 AM Ray Luo <rluo.uci.edu> wrote:
>
> > Vaibhav,
> >
> > If you meet this problem when using Amber 12, my suggestion is simply
> > upgrade to the latest version and try again. It's free to upgrade
> > AmberTools.
> >
> > 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, 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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>
>
> --
>
> 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
> _______________________________________________
> AMBER mailing list
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