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,
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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
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Received on Mon Nov 16 2020 - 05:00:02 PST
