psfgen error

From: Syed Kashif Zafar (
Date: Tue Feb 23 2010 - 22:44:21 CST

Hi all,

   I have an equilibrated pdb patch for a DMPC bilayer. Now I want to add
water and run it using NAMD.But in the pdb patch the molecules are wrapped
and when I use psfgen and topology file to generate the psf, it connects
the atoms across the periodic cell giving bonds that exist across the
periodic cell. Can anyone suggest how I can unwrap the coordinates in the
pdb that I have or some other solution.

waiting for helpful response
junior research fellow
H.E.J Research Institute
Karachi, Pakistan


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