From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Sep 25 2007 - 19:33:14 CDT

Hi all
        I figure out that there is some problem in the internal coordinate
table of NAD. I removed the IC table of NAD from topology file and now my
structure after psfgen is looking good. However I still have some doubt.
Is it safe to remove Internal coordinate table of some residue from the
topology file? also when i am taking out topology information for NAD from
the topology file
/linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
and puting it in to another file, then this new file is not working and when
i am using this file in psfgen then psfgen is complaining that atom type HN1
not found.
why is this happening? i was thinking that we can use topology of every
residue independently.

thnak you.
Dhiraj

On 9/25/07, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:
>
> 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

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