Yes, AmberTools 1.5 is the latest version of MMPBSA.py and supports energy
decomposition analysis.
-Bill
On Mon, Jun 6, 2011 at 1:12 PM, victor ma <victordsma.gmail.com> wrote:
> I'm using AMBER11 with AMBERTOOLS1.4. So i guess I need 1.5 for energy
> decomposition?
> Thanks.
>
>
>
> On Mon, Jun 6, 2011 at 12:10 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > What version of MMPBSA.py are you using? If you download the newly
> released
> > AmberTools 1.5 from the Amber website, then that version will support
> > decomposition analysis.
> >
> > -Bill
> >
> > On Mon, Jun 6, 2011 at 1:07 PM, victor ma <victordsma.gmail.com> wrote:
> >
> > > hi all
> > >
> > > I'm working on a protein-ligand binding problem and trying to get a
> > > per-residue energy decomposition. I followed the tutorial on AMBER's
> > > website, add this section into the mmpbsa.infile:
> > >
> > > &decomp
> > > idecomp=3,
> > > dec_verbose=1,
> > > /
> > >
> > >
> > > However, the run failed and it complains that it couldn't find any
> > namelist
> > > called "decomp". I checked amber11 manual. It says: "idecomp Specifies
> > > whether or not to perform a decomposition analysis. (This option is not
> > > currently supported, but will be included in a later version)". It so,
> > how
> > > do I get decomposed energies out of mmpbsa.py?
> > >
> > > THanks a lot.
> > >
> > >
> > >
> > > --
> > > Best regards,
> > >
> > > Victor
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Best regards,
>
> Victor
> _______________________________________________
> 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
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Received on Mon Jun 06 2011 - 10:30:06 PDT
