From: Dhiraj Srivastava (
Date: Tue Sep 25 2007 - 19:00:30 CDT

Hi All
        I was trying to simulate a system with NAD. i am trying to use
topology file /linux/src/vmd-1.8.6
/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp to generate
psf and pdb file. although i am able to generate psf and pdb file using
psfgen with no error but when i am loading pdb and psf file in to vmd, i am
finding a very long, unnatural bond between AC5' and AH5'. although when i
am loading PDB file alone (coming from psfgen), then i am not finding any
problem in the structure.
I tried to use stream file in psfgen but psfgen does not accept this format.
what may be the reason of getting very long bond and how can i fix the

Thank you

Dhiraj K. Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153