Re: [AMBER] MMPBSA failed

From: Albert <>
Date: Tue, 31 Jan 2017 14:36:24 +0100

Hello, My MMPBSA job still failed. Here is the information:

> mpirun -np 12 -O -i ../../infile/ -o
FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
-lp lig.prmtop -y prod*.mdcrd > & progress.log

Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /soft/amber/16/bin/mmpbsa_py_energy
cpptraj found! Using /soft/amber/16/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /soft/amber/16/bin/mmpbsa_py_energy
   calculating complex contribution...
   File "/soft/amber/16/bin/", line 100, in <module>
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/", line
218, in run_mmpbsa, self.stdout)
line 82, in run, stdout=stdout, stderr=stderr)
line 476, in run
CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
Error occured on rank 4.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4

One job means one MMPBSA job for one target. It use 12 core CPU with
MPI. I am using Amber 16+AmberTools 16

On 01/31/2017 10:38 AM, Vlad Cojocaru wrote:
> One job meaning a single MPI process, or a single job with multiple MPI
> processes ?
> Depending on the system size, grid size and number of MPI processes
> asked in 1 job, you may easily consume 64 GB .. At least that was the
> case with Amber 12 and 14 ... I know that in Amber 16 a lot of
> optimizations were done with the MMPBSA code, but we have limited
> experience thus far with Amber 16 and MMPBSA.
> All I can say is that we experienced this error often in this context
> before ... But I also know this is a generic error that can be due to
> multiple other reasons ... So, if you calculated your memory consumption
> and you found is fine within your limits, you would have to search for
> other potential issues ...
> Sorry I cannot help more ...
> Vlad

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Received on Tue Jan 31 2017 - 06:00:03 PST
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