In AmberTools 1.5, $AMBERHOME/bin/MMPBSA.py and $AMBERHOME/bin/MMPBSA.py.MPI
have been replaced by scripts called $AMBERHOME/bin/MMPBSA and
$AMBERHOME/bin/MMPBSA.MPI, respectively. You should call these scripts
directly instead of the python scripts in the source directory. This helps
to alleviate problems with using incompatible python versions with MMPBSA.
-Bill
On Mon, Sep 5, 2011 at 1:31 AM, kirtana S <skirtana4.gmail.com> wrote:
> I installed Amber tools , as I intend to use MMPBSA I did the following
> steps,
>
> cd $AMBERHOME/src/mmpbsa_py
> make install
>
> cd $AMBERHOME/test
> make test mmpbsa_py
>
> For example as in one of the tutorial :
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> -sp err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop -y *.mdcrd
>
> I could not find MMPBSA.py in $AMBERHOME/bin
>
> I used as below (assuming the flags for -rp and -lp optional)
>
> /home/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -cp complex-vac.prmtop -y md_noWAT.x
> VERSION: Command not found.
> try:: Too many arguments.
>
> It seems I did not install properly , please suggest.
>
> Thanks
> kirtana
>
> On Fri, Sep 2, 2011 at 1:53 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > MMPBSA.py allows you to specify only a complex (so no receptor or
> ligand),
> > and it will just give you the statistics for that one trajectory. If you
> > cluster your simulations and collect "folded" and "unfolded" snapshots,
> then
> > you can run MMPBSA.py on each of these clusters and get, roughly
> speaking,
> > your free energy of folding. (Be aware of MMPBSA shortcomings, though).
> >
> > HTH,
> > Jason
> >
> > On Fri, Sep 2, 2011 at 1:43 PM, KIRTANA S <skirtana4.gmail.com> wrote:
> >
> >> Hi Thomas,
> >>
> >> MMPBSA calculates the change in binding free energy of the ligand and
> >> receptor.
> >> How can I use this only for the complex only.
> >>
> >> Thanks
> >> kirtana
> >> Fri, Sep 2, 2011 at 2:43 AM, <steinbrt.rci.rutgers.edu> wrote:
> >> > Hi Kirtana,
> >> >
> >> > you can use MM-PBSA for that purpose. There is a tutorial on how to
> use
> >> it
> >> > on the Amber page plus some examples in the $AMBERHOME/src/mmpbsa
> >> > directory. But note that it will be very difficult to get the correct
> >> > ensemble for your unfolded state.
> >> >
> >> > Kind Regards,
> >> >
> >> > Thomas
> >> >
> >> > On Thu, September 1, 2011 4:09 pm, KIRTANA S wrote:
> >> >> I want to calculate the free energy change while my polymer folds.
> >> >> I have used Implicit solvent, explicit solvent and also vacuum for my
> >> >> simulation .
> >> >>
> >> >> How can I get the energy of the complex only throughout the
> simulation
> >> >> run.
> >> >>
> >> >> Thanks in advance
> >> >> kirtana
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> > Dr. Thomas Steinbrecher
> >> > formerly at the
> >> > BioMaps Institute
> >> > Rutgers University
> >> > 610 Taylor Rd.
> >> > Piscataway, NJ 08854
> >> >
> >> > _______________________________________________
> >> > 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
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 05 2011 - 14:00:13 PDT
