Re: simulating dna

From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Tue Apr 20 2010 - 14:18:51 CDT

2 issues I see:

1. par_all27_na.prm is a parameter file, not a topology
file
2. Be sure to include the path to the file, e.g. in my
Linux install it is:

topology
plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp

Hope this helps,

Ron

On Tue, 20 Apr 2010 22:32:36 +0530
  Asmita Gupta <asmita4des_at_gmail.com> wrote:
> i am trying to simulate DNA in NAMD by first creating a
>file called dna.pgn
> and writing the following lines:-
>
>
> package require psfgen
> topology par_all27_na.prm
> segment A{pdb 1bna.pdb}
> coordpdb 1bna.pdb A
> guesscoord
> writepdb dna.pdb
> writepsf dna.psf
>
> but after running the code i am getting the following
>error-
>
> ERROR: Unable to open topology file par_all27_na.prm
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to
>start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> --this problem may seem to be stupid to some experts but
>as a beginner in
> namd i am quite confused what to do.

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