On Mon, Sep 23, 2013 at 11:59 AM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi Jason,
>
> I have sent all the related files for running the MMPBSA.py.MPI program to
> you. Please take a look on those whenever you are free. Also let me know if
> you need any further information from my side.
>
The problem was in the Python parsing of the chamber topology files. I've
fixed the issue and the update is now available. If you run the following
commands:
cd $AMBERHOME && ./configure gnu
make -C AmberTools/src/parmed install
That should update your installation (the modified 'make' command will
install _just_ the ParmEd files -- if more than just update.18 are applied
to your installation you should just run "make install" to build
everything).
HTH,
Jason
Best
> sudipta
>
>
> On Mon, Sep 23, 2013 at 7:04 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > A couple more comments:
> >
> > On Sun, Sep 22, 2013 at 7:13 PM, sudipta <sudipta.mml.gmail.com> wrote:
> >
> > > [snip]
> > >
> > >
> > > Do I need to use ante-MMPBSA.py program for generating the .prmtop
> file
> > > for running MMPBSA.py.MPI program. If so how do I use that? Is there
> any
> > > significant difference between AMBERtools12 and AMBERtools13 for
> running
> > > MMPBSA.py.MPI program
> >
> >
> > No, ante-MMPBSA.py is never necessary if you create all of the needed
> > topology files in the beginning, prior to running any calculations (as is
> > recommended practice). ante-MMPBSA.py is particularly useful when you
> > decide to do MM/PBSA calculations on a system after creating the topology
> > file and you don't happen to have the files you need to create them
> through
> > tleap.
> >
> > However, ante-MMPBSA.py does _not_ work with chamber-generated topology
> > files, so that's not even an option in your case. As for the 12 vs. 13
> > difference, AmberTools 13 has more bug fixes and more stable PBSA options
> > than AmberTools 12 in terms of the default solvation radii for the
> > non-polar solvation free energy part of the calculation.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 23 2013 - 12:00:03 PDT
