From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Sep 17 2007 - 16:50:29 CDT
sorry for the incomplete previous mail. i think the problem is
something else. when i am using the vmd plugin for psfgen (so tha topology
file provided by vmd by default) then i am getting the previous problem.
when i am using toppar_all27_na_nad_ppi.str and using the script then i am
getting the error
building segment A
reading residues from pdb file m.pdb
extracted 1 residues from pdb file
Info: generating structure...
unknown atom type HN1
add atom failed in residue NAD:1
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
the atoms name in my pdb file (non hydrogen atoms) are same as in
can any one help me in solving this problem?
On 9/17/07, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:
> Hi all
> does any one has topology and parameter file for NAD+. i was using
> the same from stream (toppar_all27_na_nad_ppi.str) but i don't know why
> psfgen is making very long unnatural bond between AC5' and AH5' atoms.
> thank you
> Dhiraj K. Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
-- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
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