[AMBER] MMPBSA calculation cpptraj failed with ligand prmtop

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Thu, 21 Jan 2021 10:13:09 +0500

Dear Amber user

I am doing MMPBSA calculations on a 20ns trajectory for protein and ligand
complex. I am getting error of cpptraj failed with ligand prmtop as
mentioned below:-
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
mmpbsa_py_energy found! Using
Preparing trajectories for simulation...
2000 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand 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 475, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/rcms/Downloads/Amber/amber20/bin/cpptraj failed with
prmtop G6P_n.prmtop!

I am new in doing this calculation, could anyone please help me to figure
out the problem why I am getting this error and how should I fix it. Any
suggestion would really be appreciated.
Thanks in advance.
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Received on Wed Jan 20 2021 - 21:30:02 PST
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