From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Mon Sep 22 2014 - 14:53:04 CDT
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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