you can check the AMBER14 manual also, it has a pretty good section on
MMPBSA.py
One critical thing is to make sure you put in the implicit information in
the mmpbsa.in file. That is, you need to tell it what implicit solvent
model you are using, and the parameters for that model.
On Sun, Nov 9, 2014 at 9:10 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Nov 9, 2014 at 1:26 AM, Bajarang Kumbhar <
> kumbharbajarang.gmail.com>
> wrote:
>
> > Hi Dear AMBER USERS
> > I have perform the Implicit simulation of protein and
> > drug molecule, Further i would like to calculate the binding energy using
> > MMPBSA and GB method but the most of tutorial show the explicit
> simulation
> > data for MMPBSA/GB calculation.
> > like this
> >
> > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> > ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop
> -y
> > *.mdcrd.
> >
> > my question is that, it is possible to perform the PB and GB calculation
> > without the solvated.prmtop file.
> >
>
> Yes. The solvated prmtop is only used to strip solvent and ions from the
> trajectory file. If you do not provide a solvated topology file, MMPBSA.py
> will assume that you do not need to strip solvent and ions and will simply
> run the calculation directly (but then, of course, the input trajectory
> needs to be compatible with the complex topology file).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Nov 09 2014 - 12:00:02 PST
