[MMTK] Potential Energy: NaN issue

Reginald Smith rsmith at sloan.mit.edu
Thu Jan 31 17:58:51 UTC 2013


Ok, sorry I was trying to find out if MMTK could calculate the approximate
minimum free energy profile *ab initio* from a sequence. Is there a way to
do this with MMTK or should I try another tool? Thanks.
Reggie


On Mon, Jan 28, 2013 at 10:43 AM, Konrad Hinsen <
research at khinsen.fastmail.net> wrote:

>
>  > AAAAA. However, that (and any other sequence I tried) kept giving
> potential energy and
>  > gradient results of not-a-number (NaN). Below is my code and any help
> is appreciated.
>  >
>  > # Create one peptide and calculate energy
>  > universe = InfiniteUniverse(Amber94ForceField())
>  > universe.peptide = PeptideChain('AAAAA',n_terminus=0,c_terminus=0)
>
> If you create a peptide chain from just its sequence, it has no
> conformational data. You then calculate the energy for a system with
> undefined
> positions, which explains the NaN values.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: research AT khinsen DOT fastmail DOT net
> http://dirac.cnrs-orleans.fr/~hinsen/
> ---------------------------------------------------------------------
>



-- 
Reginald Smith (史瑞吉)
rsmith at sloan.mit.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://starship.python.net/pipermail/mmtk/attachments/20130131/b7e6303b/attachment.html>


More information about the mmtk mailing list