Re: FEP setup

From: Chris Chipot (
Date: Wed Dec 28 2005 - 17:21:28 CST


there are two routes that will answer your question. Once you have
defined your dual topology, i.e. a topology that contains both the
initial and the final states of the transformation, you can either
add a patch to remove the superfluous valence angles and torsions,
and hence get a correct PSF (this is what CHARMM aficionados would
do) or generate an incorrect one using PSFGen and correct it based
on the info contained in the .fep file required for the alchemical
transformation (-1 for vanishing atoms, +1 for appearing atoms and
0 otherwise) using ALCHEMIFY, which you can find on the NAMD site.

Chris Chipot


Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex


      To sin by silence when we should protest makes cowards out of men
                                                    Ella Wheeler Wilcox

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:28 CST