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.
However, the MMPBSA.py.MPI program is not running
On Mon, Sep 23, 2013 at 2:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Mon Sep 23 2013 - 17:00:02 PDT
