Dynamics with a glycerol molecule

From: Lucio Montero (lucioric_at_ibt.unam.mx)
Date: Mon Apr 07 2008 - 17:34:39 CDT

I want to run a MD of a protein with a glycerol molecule that appears in the
protein pdb file as a GOL residue. When I run the psfgen module, there
appears that there are not a topology defined for the GOL residue. Do I have
to create a new residue on the topology file, or can I do anything else,
because I don’t know the standard bonding distances for the glycerol?.

 

 

Lucio Montero

Laboratorio de Federico Sánchez

Ext. 27666

Instituto de Biotecnología, UNAM

Cuernavaca, Morelos, México

 

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