Re: [AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop

From: Ray Luo <>
Date: Fri, 27 Mar 2020 09:35:16 -0700


Looks like your computer doesn't have enough memory. You may change
the grid spacing twice as large from 0.5 A to 1.0 A by inserting


into the pb namalist section of the input file.

All the best,
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Fri, Mar 27, 2020 at 9:13 AM <> wrote:
> 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, 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/", line 100, in <module>
>     app.run_mmpbsa()
> File "/soft/amber/amber18/lib/python2.7/site-packages/MMPBSA_mods/", line 218, in run_mmpbsa
>, self.stdout)
> File "/soft/amber/amber18/lib/python2.7/site-packages/MMPBSA_mods/", line 82, in run
>, stdout=stdout, stderr=stderr)
> File "/soft/amber/amber18/lib/python2.7/site-packages/MMPBSA_mods/", 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,
> Azahara.
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Received on Fri Mar 27 2020 - 10:00:02 PDT
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