FEP setup

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Dec 27 2005 - 11:43:53 CST

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Hi all,
 
 I'm trying to setup an FEP calculation for a hexasaccharide going to a pentasaccharide. I've got the coordinates for the hexasaccharide and I know which atoms have to "vanish", but I am having difficulty generating a psf file for the calculation. I've "marked" the atoms in my pdb file which I want to "go away" and I've added a hydrogen. The problem lies in my topology file, I believe, but I'm not sure how to set it up.
 
 Basically, I've got 6 sugar residues and five patches versus 5 residies and four patches. How does one set this up so one gets the correct topology to give the correct psf? It's obvioulsly more complicated than just adding a hydrogen to the pdb file.
 
 TIA,
 Richard
 
Richard L. Wood, Ph. D.
 Computational Chemist
 Cockeysville, MD 21030
 rwoodphd_at_yahoo.com

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