VMD-L Mailing List

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Tue Oct 02 2007 - 14:53:47 CDT

Hello,
I am having some problem in running namdenergy.
I am doing the text version as:
.................................................................................
vmd -dispdev text -psf x.psf -pdb x.pdb -dcd x.dcd
.................................................................................

and my script is:source x.tcl
.............................................................................................................................
package require namdenergy
set sel1 [atomselect top protein]
set sel2 [atomselect top "water and same residue as within 4 of protein"]
for {set i 0} {$i < [molinfo top get numframes]} {incr i} {
$sel1 frame $i
$sel2 frame $i
namdenergy -sel $sel1 $sel2 -elec -par par_all27_prot_na.prm -extsys
x.xsc-pme -ofile elect1 -switch 10 -cutoff 12
}
...............................................................................................................................

but when its done, i don't see any output file (i gave the option of output
file "-ofile elect1").
 Please let me know what i am missing in the script.
Thank you
singh