VMD-L Mailing List

From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Tue Feb 08 2011 - 20:48:50 CST

Marc:

For compatibility reasons (I run on different machines and cannot guarantee
even the same user name on different sites) I define an environment variable
NAMD_TOPPAR everywhere (in my .tcshrc files ) with something like

setenv NAMD_TOPPAR /home/marc/namd/toppar

In the vmd script, I then do

topology $env(NAMD_TOPPAR)/top_all27_prot_na_carb.rtf

The tcl env() command evaluates environment variables. You need the $
to obtain the value (not the reference). If you plan to put the topology
files in a fixed place for this tutorial, then you can just point to it directly:

topology /home/marc/tutorial/toppar/top_all27_prot_na_carb.rtf

Good luck,

Mark Cunningham
The University of Texas-Pan American

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Marc Charendoff
Sent: Tuesday, February 08, 2011 12:26 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: psfgen script for VMD 1.8.7

Hello,

      I am in the middle of trying to get a script to run in the VMD 1.8.7 TkCon as part of a tutorial. The tutorial involves setting up an MD run with a DNA-Protein complex. The body of the script looks ok but the beginning must be wrong as I get the error "Unable to open topology file top_all27_prot_na_carb.rtf". Is there another topolgy file I need to specify within VMD? Or can I reset path to the NAMD toppar directory where these topologies reside?
Guidance for this novice appreciated.

Thanks, Marc

1dnk.pgn first two lines ......

package require psfgen

topology top_all27_prot_na_carb.rtf