From: L. Michel Espinoza-Fonseca (
Date: Tue Sep 25 2007 - 19:33:46 CDT

Hi Dhiraj,

You should try to minimize the energy of the system first and see if
this bond disappears. Sometimes it happens that the geometry appears
to be incorrect but after minimization everything is ok.

If you observe that bond after energy minimization, then I would
recommend you to use the standalone version of psfgen and apply
"regenerate angles dihedrals" right after the NAD segment.


2007/9/25, Dhiraj Srivastava <>:
> 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
> problem?
> Thank you
> --
> Dhiraj K. Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153