Dear Ray and Amber developers,
Thanks for the suggestion.
It turns out that Amber directory structure has changed since these
suggestions were made in 2011.
There is no sander folder in $AMBERHOME/src folder in Amber18 as suggested
in the old post (which is probably for Amber10).
I also searched in AmberTools/src/, where I get mdread.F90 which I is not
the same as mdread.f (right?).
Additionally, I just got access to Amber20 which I am planning to install
over the weekend.
Thus, it would be really helpful if someone using either Amber18 or Amber20
can suggest me on this.
Should I expect a similar error with Amber20 and if yes, where should I
make these changes about new atom type information?
Do I need to recompile after these changes are made, the older post doesn't
mention about this.
Thank you very much for responding.
Best regards.
On Fri, Dec 4, 2020 at 10:11 AM Ray Luo <rluo.uci.edu> wrote:
> Vaibhav ,
>
> Google amber mmpbsa "Bad atom type" gives the following suggestions:
>
> http://archive.ambermd.org/201902/0241.html
> http://archive.ambermd.org/201111/0370.html
>
> 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 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> >
> > 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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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
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Received on Thu Dec 03 2020 - 21:30:02 PST
