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
Prod.crd
Loading and checking parameter files for compatibility...
/home/rcms/Downloads/Amber/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/rcms/Downloads/Amber/amber20/bin/cpptraj
mmpbsa_py_energy found! Using
/home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
2000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
File "/home/rcms/Downloads/Amber/amber20/bin/MMPBSA.py", line 100, in
<module>
app.run_mmpbsa()
File
"/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
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.
Regards
Sadaf
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Received on Wed Jan 20 2021 - 21:30:02 PST
