[AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 14 Dec 2020 15:31:52 +0900

Dear All,
I'm getting the following error message while trying to run MMPBSA.py in
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
  startframe=1, endframe=100, interval=5,
  verbose=2, keep_files=2, netcdf=1, receptor_mask=2-386,
  igb=5, saltcon=0.150,
  istrng=0.15, fillratio=4.0,
  idecomp=1, print_res="56-57; 74-75; 167; 222; 225-227; 229-231; 272-273;
275-277; 336; 368; 370; 372-373"

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
Loading and checking parameter files for compatibility...
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>
line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
line 156, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/exx/Downloads/amber20/bin/sander failed with prmtop
Exiting. All files have been retained.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Mon Dec 14 2020 - 02:30:02 PST
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