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