Hi,
I am using Amber 10. Can I use the AmberTool1.5 with Amber10 or it is only
compatible with Amber11.
Hirdesh
On Mon, Jun 6, 2011 at 10:44 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 06 2011 - 20:30:02 PDT
