On Wed, Mar 23, 2016 at 6:49 AM, Annie Ancy <ancy.annie42.gmail.com> wrote:
> Dear all,
>
> Am doing MMPBSA calculation and i got following error. I dont
> know how to fix this issue. Please help me to find the solution.
>
> My input file is,
>
> Input file for running PB and GB in serial
> &general
> endframe=5000, keep_files=2, startframe=1,
> /
> &gb
> igb=1, saltcon=0.100,
> /
> &pb
> inp=1, radiopt=0
> istrng=0.100,
> /
>
> and the output error is,
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /home/others/kumar/amber14/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> File "/home/others/kumar/amber14/bin/MMPBSA.py.MPI", line 96, in ?
> app.run_mmpbsa()
> File "/home/others/kumar/amber14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/home/others/kumar/amber14/bin/MMPBSA_mods/calculation.py", line
> 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/home/others/kumar/amber14/bin/MMPBSA_mods/calculation.py", line
> 415, in run
> raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/others/kumar/amber14/bin/mmpbsa_py_energy failed with
> prmtop com.prmtop!
>
>
> Error occured on rank 89.
>
​Look in _MMPBSA_receptor_gb.mdout.89 and see if there is an error message
there.
In general, a good first step in debugging is to use a smaller number of
frames (like 2 or 3 frames) and try running in serial. From the error
message here, it's clear you are running at least 90 threads in MPI. While
that *shouldn't* cause a problem, I don't know that mpi4py (the MPI used by
MMPBSA.py) is frequently tested to such a large scale.
HTH,
Jason
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 23 2016 - 06:30:03 PDT
