OK, I have some reading to do, then :D
On Tue, Jun 25, 2013 at 7:28 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Jun 24, 2013 at 7:39 PM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I have minimized a structure in vacuum and now I want to compute its
> normal
> > modes. I want to use the 'nmode' command line tool, but I don't know what
> > control parameters do I have to pass in the "nmdin" file. I have tried to
> > find these in the Amber user's guide and AmberTools, with no luck.
> >
> > Please, any help is very much appreciated.
> >
>
> There is a chapter on nmode in the Amber 9 manual (no later ones to my
> knowledge, but nmode has changed very little for a _very_ long time).
>
> Currently the preferred way of carrying out normal mode calculations is to
> use the nmode() function in NAB. The NAB language reference is given its
> own chapter for molecular mechanics functionality in the AmberTools manual,
> and you can look at $AMBERHOME/src/mmpbsa_py/mmpbsa_entropy.nab for an
> example of how to use NAB to both minimize and compute normal modes at
> once.
>
> HTH,
> Jason
>
> P.S. The hidden gateway to the Amber 9 manual can be found
> here<http://ambermd.org/doc9/>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Jun 25 2013 - 07:30:02 PDT
