VMD-L Mailing List

From: Balazs Jojart (jojartb_at_gmail.com)
Date: Sun Jan 17 2010 - 05:11:07 CST

Dear Users,
I have a problem during trajectory evaluation.
A would like to measure distance between two atoms in the trajectory.
I know, that without deleting the selection, variables I can shock my
computer.
Here is a part of my tcl script:

mol new {../1.00M_GPCR_ions.pdb} type {pdb} first 0 last -1 step 1 waitfor 1
mol addfile {../1.00_PROD3_CASE1.dcd} type {dcd} first -1 last -1 step
1 waitfor -1 0
set outfile1 [open 1.00_PROD1_Asp52OD1_NA_min.txt w]
set nf [molinfo top get numframes]
for {set i 1} {$i < $nf} {incr i} {
    puts "frame $i of $nf"
    set selatoms1 [[atomselect top "protein and resid 52 and name OD1 or
resname NA and resid 1"] get index]
    set bond1 [list [lindex $selatoms1 0] [lindex $selatoms1 1]]
    set d1 [measure bond $bond1 frame $i]
    $selatoms1 delete
    $bond1 delete
    set selatoms2 [[atomselect top "protein and resid 52 and name OD1 or
resname NA and resid 2"] get index]
    set bond2 [list [lindex $selatoms2 0] [lindex $selatoms2 1]]
    set d2 [measure bond $bond2 frame $i]
........
}

Unfortunatelly, I obtain the following error:
> frame 1 of 7151
> invalid command name "790 4926"
> Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
> Info) Exiting normally.
Where is the problem in my script, and how can I solve it?
Any help will be appreciated!
Thank you for your help in advance,
Balazs