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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Received on Thu Dec 03 2020 - 09:00:03 PST
