Dear All,
I'm getting the following error message while trying to run MMPBSA.py in
Amber20.
It says that the receptor mask overwritten with default, which I don't know
why it is doing even after I gave a specific receptor mask (1st residue is
my ligand in the trajectory). It also gives the bad atom type error, that
I got with Amber18 last month.
>From the output files (attached), it is not clear what is the exact nature
of the error, thus I have no clue how to proceed to fix the same.
Can you please help me understand why the dry prmtop is not compatible?
And how can I possibly attempt to get this analysis done?
My mmpbsa input file is given below.
Thanking you all in advance.
Best regards
mmpbsa input file:
(base) [exx.c107739 mmpbsa-6701-tyr]$ more 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,
/
Error message on the terminal
(base) [exx.c107739 mmpbsa-6701-tyr]$ MMPBSA.py -O -i mmpbsa-decomp.in -o
mmpbs-rouf-6701-tyr.dat -do decomp-rouf-6701-tyr.dat -sp
../rouf-6701-tyr-solv.prmtop -cp ../rouf-6701-tyr-dry.prmtop -lp
../tyr-dry.prmtop -y ../rouf-6701-tyr-solv-prod300.nc -rp
../rouf-6701-nolig-dry.prmtop
Loading and checking parameter files for compatibility...
*/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py:603:
UserWarning: receptor_mask overwritten with default*
warnings.warn('receptor_mask overwritten with default\n')
cpptraj found! Using /home/exx/Downloads/amber20/bin/cpptraj
sander found! Using /home/exx/Downloads/amber20/bin/sander
Preparing trajectories for simulation...
20 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/exx/Downloads/amber20/bin/sander
calculating complex contribution...
* bad atom type: M1*
File "/home/exx/Downloads/amber20/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/exx/Downloads/amber20/bin/sander failed with prmtop
../rouf-6701-tyr-dry.prmtop!
Exiting. All files have been retained.
--
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
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Mon Dec 14 2020 - 02:30:02 PST
