Thank you for information sir,
while removing the zero in the section DIHEDRAL_PERIODICITY of .prmtop
file particular " 0.00000000E+00 "
1.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00
3.00000000E+00
3.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00
1.00000000E+00
1.00000000E+00 2.00000000E+00 0.00000000E+00 2.00000000E+00
0.00000000E+00
2.00000000E+00 3.00000000E+00 0.00000000E+00 0.00000000E+00
2.00000000E+00
3.00000000E+00 3.00000000E+00 0.00000000E+00 2.00000000E+00
2.00000000E+00
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
made like this all parmtop solavted, complex, receptor
3.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00
1.00000000E+00
1.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00
2.00000000E+00 3.00000000E+00
3.00000000E+00 3.00000000E+00
2.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
still facing error
python2.7 /opt/amber16/bin/MMPBSA.py -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp FULL-AG13-ONE.top -cp complex.prmtop -rp
receptor.prmtop -lp ligand.prmtop -y LAST5NS-FULL-AG13-ONE.dcd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
File "/opt/amber16/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
157, in run
self.prmtop))
CalcError: */opt/amber16/bin/mmpbsa_py_energy failed with prmtop
complex.prmtop!*
Exiting. All files have been retained.
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Received on Thu Dec 12 2019 - 04:00:02 PST
