Thank you for your suggestion, Jason.
At the end of the file there was an informative "Requested charges to be
read in, but found none". I revised my topology creation scheme (I'm using
gromacs to run the MD simulations and AMBER for MM/PBSA, so I have to
convert some files.) and the ligand charge information was indeed missing.
The calculations are running perfectly now.
Thank you again
Best regards,
Leandro
On Thu, Aug 25, 2016 at 2:35 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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 - 13:00:03 PDT
