[AMBER] error during MMPBSA calculation -reg.

From: Jeyaram R A <ra.jeyaram.vit.ac.in>
Date: Thu, 11 Jan 2018 07:06:16 +0000

Dear all,

        I follow the AMBER ADVANCED TUTOTORIAL - 3, SECTION 3.2 for the binding free energy calculation of the protein - ligand complex by MMPBSA method. During the calculation, it shows the error due to the topology of the receptor protein. The error lines are given in the following

[Jeyaram.DBTSASKV MMPBSA]$ MMPBSA.py -O -i mmpbsa.in -o 1.dat -sp solvated.prmtop -cp complex.prmtop -lp ligand.prmtop -rp protein.prmtop -y md1.nc
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /usr/local/bin/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/bin/amber16/bin/cpptraj
Preparing trajectories for simulation...
1000 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /usr/local/bin/amber16/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  File "/usr/local/bin/amber16/bin/MMPBSA.py", line 100, in <module>
  File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 478, in run
CalcError: /usr/local/bin/amber16/bin/cpptraj failed with prmtop protein.prmtop!
Exiting. All files have been retained.
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Received on Wed Jan 10 2018 - 23:30:02 PST
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