Re: Problem with running namdenergy plugin from text interface

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Sep 22 2014 - 15:09:10 CDT

Hi Zeynab,
Instead of "package provide namdenergy 1.4", could you try "package
require namdenergy"? The two have different behaviors (read about them:
http://wiki.tcl.tk/1491), and you chose the wrong one. The reason it
works if you don't run it using -e is that then VMD has loaded all of
its packages, and namdenergy exists. From the text interface, all
plugins need to be loaded explicitly with the appropriate package
require command.
-Josh Vermaas

P.S. Have you tried the 1.9.2 beta? Alot of improvements have been made
since 1.9, and while this error wasn't 1.9 specific, there were many
features that have been significantly improved and added since then.

On 09/22/2014 02:53 PM, zeynab mohamad hoseyni wrote:
> Dear all,
>
> I run namdenergy using the following tcl script (calling
> run-namdenergy.tcl):
> set nfiles 10
> set str ./protein.psf
> for {set j 1} {$j <= $nfiles} {incr j} {
> mol new $str type psf waitfor all
> mol addfile glp1r_NPT-red_$j.dcd type dcd waitfor all
> package provide namdenergy 1.4
> set sell [atomselect top "protein"]
> set out out$j
> namdenergy -nonb -conf -sel $sell -cutoff 12 -switch 10 -pme -extsys
> namd-generated2.xsc -ofile $out -par par_all36_prot.prm
> mol delete all
> }
>
> Whenever I source the tcl within vmd tkConsole the script works
> but as soon as I use the following command
> vmd -dispdev text -e run-namdenergy.tcl
> I receive this error:
>
> Info) Dynamically loaded 3 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUX/molfile
> vmd > package provide namdenergy 1.4
> vmd > namdenergy
> invalid command name "namdenergy"
>
> I use vmd version 1.9. Can any one guide me?
>
> Thanks in advance,
> Zeynab
>
>
>
>
>
>

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