Hi Jason,
another problem which I am facing during mmpbsa calculation. it is showing
that the number of atoms in .prmtop file mismatches with the no of atoms in
.inpcrd file which is generated by mmpbsa.py program.
FATAL: NATOM mismatch in coord and topology files
However, I am not clear about this. Please give some suggestions regarding
this.
On Mon, Sep 23, 2013 at 7:16 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Sep 23, 2013, at 8:11 PM, sudipta <sudipta.mml.gmail.com> wrote:
>
> > Version is reported as <version>.<patches applied>
> >
> > AmberTools version 13.18
> > Amber version 12.19
> >
> > yes, the MMPBSA.py passes the test run. I can see all of those outputs
>
> Now try running your calculation in serial instead of parallel. Also,
> don't just say "it didn't run". Give exact input and output, as per usual
> debugging procedure.
>
> All the best,
> Jason
>
> >
> >
> > On Mon, Sep 23, 2013 at 7:56 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> On Mon, Sep 23, 2013 at 7:36 PM, sudipta <sudipta.mml.gmail.com> wrote:
> >>
> >>> Do I need to download ambertools13. I have not done that. Rather, I ran
> >> the
> >>> commands that you mentioned in the previous mail. However, the second
> >>> command line didn't work and I just use the 'make install' for that.
> >>> Moreover, i used -mpi flag in the first command line to install the MPI
> >>> version of that.
> >>
> >> Check the output of
> >>
> >> $AMBERHOME/update_amber --version
> >>
> >> What does it say?
> >>
> >> Do the MMPBSA.py tests pass? (Go to $AMBERHOME/AmberTools/test and run
> the
> >> command "make test.mmpbsa").
> >>
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
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Received on Sat Oct 12 2013 - 11:00:02 PDT
