[AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop

From: <Azahara.Doncel.uv.es>
Date: Thu, 12 Mar 2020 16:58:17 +0100 (CET)

Dear All,

We have used the MM-PBSA method to calculate the binding free energy for the association of two monomers.

The monomer was parametrized based on the General Amber Force Field, GAFF (gaff.dat). The partial charges for the monomer atoms were calculated with the AM1-BCC method using the antechamber module of AmberTools. To create the topology files of the dimer in solution, the dimer in vacuum and the monomers in the gas phase, tleap of AmberTools module was used.
Then, we carried out the binding energy calculation using script MMPBSA.py, but an error has occurred while executing it.

And the message we get when we run the script:

Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /soft/amber/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /soft/amber/amber18/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning PB calculations with /soft/amber/amber18/bin/mmpbsa_py_energy
  calculating complex contribution...
*** Error in `/soft/amber/amber18/bin/mmpbsa_py_energy': malloc(): memory corruption: 0x000000000181e3d0 ***
File "/soft/amber/amber18/bin/MMPBSA.py", line 100, in <module>
File "/soft/amber/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
File "/soft/amber/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
File "/soft/amber/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /soft/amber/amber18/bin/mmpbsa_py_energy failed with prmtop complex_vacuum.prmtop!

I dont know where the problem is. I would be really appreciated it if anyone can help me..

Best regards,

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Received on Thu Mar 12 2020 - 09:00:03 PDT
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