On Mon, Jun 13, 2011 at 3:11 PM, David Cantu <cantudav.gmail.com> wrote:
> Thank you...
>
> Ive used Amber before, but never done Normal Mode Analysis. Is the nab code
> available in Amber11/AmberTools1.4?
>
Yes. You can look at the program
$AMBERHOME/AmberTools/src/mmpbsa_py/mmpbsa_entropy.nab in AmberTools 1.5 as
an example program (written by Dwight Mcgee).
Note that the functionality is available in AmberTools 1.4, but mmpbsa_py
wasn't moved over to AmberTools until version 1.5. You can also build
AmberTools 1.5 alongside Amber 11.
HTH,
Jason
>
>
> On Wed, Jun 8, 2011 at 11:48 AM, David A. Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Jun 08, 2011, David Cantu wrote:
> > >
> > > To Everyone: I cannot find a section of nmode on the Amber11 and
> > AmberTools
> > > 1.4 User's Manual.
> >
> > Nmode is a very old program, and the only reason we still distribute it
> is
> > for
> > use with some older mm-pbsa scripts. In all respects, the nab code is
> what
> > you should be using.
> >
> > ...good luck...dac
> >
> >
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> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 13 2011 - 15:00:02 PDT
