[MMTK] Nan for Energy and Gradients

khinsen at cea.fr khinsen at cea.fr
Fri Nov 25 12:01:31 CET 2005


On 24.11.2005, at 10:49, vanitha at cs.wisc.edu wrote:

> I have a simple Python file that computes the energy and gradient of a
> protein 1bp2.pdb (Correct fold from the DecoysR'Us database. I get  
> nan for
> both the energy and the gradient. Do any of you have any thoughts  
> on why

I can't check because I am not in the office today, but the most  
frequent cause is missing atom positions in the PDB file. You can  
check this with code like

	for atom in universe.atomList():
		if atom.position() is None:
			print atom.fullName(), " has an undefined position"

Konrad.
--
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Konrad Hinsen
Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
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