On Fri, Sep 4, 2015 at 3:12 AM, sunita gupta <sunita.bio.gmail.com> wrote:
> Hello all,
>
> I am trying to run MMPBSA.py.MPI of AmberTools 14. The mmpbsa.in file
> includes parameters for pb and nmode calculations.
>
> *mmpbsa.in <http://mmpbsa.in> >>*
> Input file for running PB and NM
> &general
> startframe=1, endframe=100, keep_files=2, strip_mask=":WAT:Na+"
> /
> &pb
> istrng=0.100, exdi=80.0, indi=2.0,
> /
> &nmode
> nmstartframe=1, nmendframe=10, nminterval=1, nmode_istrng=0.1,
> /
>
Do you have other ions besides Na+ in your system? I suspect you do,
because MMPBSA.py is trying to interpret coordinate lines as unit cell
dimensions, for some reason. It's hard for me to tell why this is
happening...
You should be able to get a more sensible error message if you put
"netcdf=1" in your &general section (to force the use of NetCDF internal
trajectories instead of ASCII versions, which don't have this problem). My
suspicion is that strip_mask is not removing enough atoms, so the
trajectory file is not matching the topology file.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 04 2015 - 04:30:04 PDT
