VMD-L Mailing List

From: Simpson, Lisa M (lmsimp_at_essex.ac.uk)
Date: Thu Mar 20 2008 - 12:38:36 CDT

Dear VMD users,

A few years ago someone put a post out about a script called a2adist.tcl (see below)
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2805.html

I have tried running it but have had no luck. I keep a vecsub error when I execute-

vmd > set A [atomselect top "index 1000"]
atomselect0
vmd > vmd > set B [atomselect top "index 3000"]
atomselect1
vmd > source a2adist.tcl
vmd > a2adist $A $B

vecsub: non-numeric in first argument

I don't suppose you know what I'm doing wrong?
Any help would be greatly appreciated.

Thanks.

Lisa.

a2adist.tcl
---------------------------------------------------------

proc a2adist {A B} {
        set nf [molinfo top get numframes]
        set outfile [open adist.txt w]
        puts $outfile "Frame# A2A_Distance"
        for {set i 0} {$i < $nf } { incr i } {
                set posA [$A get {x y z}]
                set posB [$B get {x y z}]
                set dist [vecdist $posA $posB]
                puts $outfile "$i $dist"
        }
        close $outfile
}

---------------------------------------------------------

OLD POSTS:

Hi Jerry,

You can save below procedure into a file (i.e. a2adist.tcl) and call it vmd
tkon shell.

To make it work type in vmd tkon shell:

set atomA [atomselect top "index 555"]
set atomB [atomselect top "index 666"]
source a2adist.tcl
a2adist atomA atomB

You can also make extra calculation within for loop.

----Procedure----
proc a2adist {A B} {
        set nf [molinfo top get numframes]
        set outfile [open adist.txt w]
        puts $outfile "Frame# A2A_Distance"
        for {set i 0} {$i < $nf } { incr i } {
                set posA [$A get {x y z}]
                set posB [$B get {x y z}]
                set dist [vecdist $posA $posB]
                puts $outfile "$i $dist"
        }
        close $outfile
}
==========ABC==========
Ahmet Bakan
Chemistry, Junior
Koc University
abakan_at_ku.edu.tr
ICQ #86167698
http://home.ku.edu.tr/~abakan

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Jerry Ebalunode
Sent: Thursday, May 06, 2004 11:18 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: measuring distances in vmd tkon

Hi all,

Which commands or set of commands could one use in measuring distances
between two atoms and if possible monitoring this property over a
trajectory
and writing it to disk for later examination, within the vmd tkon shell.

Thanks for any help in advance.