From: Sadaf Rani <sadafrani6.gmail.com>
Date: Fri, 12 Feb 2021 18:13:17 +0500

---------- Forwarded message ---------
From: Sadaf Rani <sadafrani6.gmail.com>
Date: Thu, 11 Feb 2021 at 17:57
Subject: MMPBSA Error
To: AMBER Mailing List <amber.ambermd.org>

Dear Amber

I am getting an error of raise CalcError('%s failed with prmtop %s!' %
(self.program,) while doing MMPBSA calculation in amber.
I am doing the command as following:-
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp complex.prmtop
-cp complexdry.prmtop -rp protein_cofactordry.prmtop -lp G6P_n.prmtop -y
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/rcms/Downloads/Amber/amber20/bin/cpptraj
sander found! Using /home/rcms/Downloads/Amber/amber20/bin/sander
Preparing trajectories for simulation...
2000 frames were processed by cpptraj for use in calculation.

Running calculations on a normal system...

Beginning GB calculations with /home/rcms/Downloads/Amber/amber20/bin/sander
  calculating complex contribution...
  File "/home/rcms/Downloads/Amber/amber20/bin/MMPBSA.py", line 100, in
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/rcms/Downloads/Amber/amber20/bin/sander failed with prmtop
Exiting. All files have been retained.

In all of the solvated and dry complex and protein I have neutralized the
system with counter Na+ ions however in mmpbsa.in file I am using strip
mask for both WAT and Na+ but still I get error of NATOM mismatch in
complex_gb.mdout file as below:-

FATAL: NATOM mismatch in coord and topology files
I am still unable to figure out the source of difference. Could anyone
suggest to me how I should fix this problem? Please find attached files.

Many thanks in advance.

AMBER mailing list

Received on Fri Feb 12 2021 - 05:30:03 PST
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