[MMTK] Potential Energy: NaN issue

Konrad Hinsen research at khinsen.fastmail.net
Mon Jan 28 15:43:11 UTC 2013

 > 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 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

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