Hello!
In our computing center, we have Amber 11 and Amber 12 available. Amber
11 has been built with PGI and Amber 12 with Intel 12.1.2.
I tried running an MMPBSA study on a certain set of topology/trajectory
files. While keeping the input constant, using MMPBSA from AmberTools
1.5 the analysis works. Using MMPBSA.py from AmberTools 12,
mmpbsa_py_energy crashes with a CalcError:
> Running command:
> time MMPBSA.py -O -i mmpbsa_100frames.in -cp ../complex_unsolvated.prmtop -sp ../top.prmtop -rp ../receptor.prmtop -lp ../ligand.prmtop -y ../production_NVT.mdcrd
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /sw/global/applications/amber/12/bin/mmpbsa_py_energy
> cpptraj found! Using /sw/global/applications/amber/12/bin/cpptraj
> Preparing trajectories for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Beginning PB calculations with /sw/global/applications/amber/12/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /sw/global/applications/amber/12/bin/mmpbsa_py_energy failed with prmtop ../complex_unsolvated.prmtop!
> Exiting. All files have been retained.
> Command exited with non-zero status 1
I then used use_sander = 1. Sander then threw the same error:
> Running command:
> time MMPBSA.py -O -i mmpbsa_100frames.in -cp ../complex_unsolvated.prmtop -sp ../top.prmtop -rp ../receptor.prmtop -lp ../li
> gand.prmtop -y ../production_NVT.mdcrd
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> sander found! Using /sw/global/applications/amber/12/bin/sander
> mmpbsa_py_energy found! Using /sw/global/applications/amber/12/bin/mmpbsa_py_energy
> cpptraj found! Using /sw/global/applications/amber/12/bin/cpptraj
> Preparing trajectories for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Beginning PB calculations with /sw/global/applications/amber/12/bin/sander
> calculating complex contribution...
> CalcError: /sw/global/applications/amber/12/bin/sander failed with prmtop ../complex_unsolvated.prmtop!
> Exiting. All files have been retained.
> Command exited with non-zero status 1
I've seen this error several times on the mailing list. I was not able
to find any single thread explaining the origin of this error and the
solution to it. Towards the end of this thread:
http://archive.ambermd.org/201207/0137.html the discussion is about
compilers, but without any further comment of the developers and without
conclusion.
I think we should clarify where the error really comes from and if it
could possibly be solved in the code. I would be happy to help with some
more testing in the future.
Thanks,
Jan-Philip
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Received on Wed Aug 29 2012 - 05:30:03 PDT
