On Wed, Aug 29, 2012 at 8:11 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> 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.
>
To be honest, I'm not sure where the error is coming from. Error messages
in this case seem to be swallowed up (unless they aren't -- are there any
errors printed out in the _MMPBSA_complex_pb.mdout.0 file?). There were
significant changes to PBSA, and my guess is you're hitting a bomb in the
code that is forcing a bail-out. Since the PBSA code used by sander and
NAB are the same, I would not expect use_sander to fix this.
The best bet, IMO, would be to run the energy calc for your complex by
hand, and see if MMPBSA.py is inadvertently squashing the error message (in
which case, this should be fixed). The command for PB should be:
mmpbsa_py_energy -O -i _MMPBSA_pb.mdin -p <complex_prmtop> -c
_MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
(mdcrd replaced by nc if you use netcdf intermediates).
I'd be interested to see what you learn.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 29 2012 - 07:30:04 PDT
