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 - 04:30:04 PDT
