On Thu, Aug 25, 2016 at 10:43 AM, Leandro Bortot <leandro.obt.gmail.com>
wrote:
> Dear users,
>
> I searched the list and couldn't find an answer to this problem.
> Related errors were on the MPI version while I use the serial version.
> I'm trying to run a MMPBSA calculation in which MMPBSA.py gives an
> error only when calculating the ligand contribution. This doesn't make
> sense to me since the complex contribution is calculated normally and all
> prmtops were created together in tleap.
> Do you have any suggestions about how to solve this? The output is
> below.
>
>
>
> Loading and checking parameter files for compatibility...
> sander found! Using /path_to_amber16/bin/sander
> cpptraj found! Using /path_to_amber16/bin/cpptraj
> Preparing trajectories for simulation...
> 1 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning PB calculations with /path_to_amber16/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> File "/path_to_amber16/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File "/path_to_amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/path_to_amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/path_to_amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 431, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /path_to_amber16/bin/sander failed with prmtop lig.0.prmtop!
>
​Check the _MMPBSA_ligand_pb.mdout.0 file -- do you see an error message
that may indicate what happened?
HTH,
Jason
--
Jason M. Swails
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Received on Thu Aug 25 2016 - 11:00:04 PDT
