Re: NAD topology and parameter file

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Sep 17 2007 - 16:50:29 CDT

Hi all
        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
toppar_all27_na_nad_ppi.str file.
can any one help me in solving this problem?

thank you
Dhiraj

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
>
> --
> 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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