VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Jan 24 2008 - 16:39:40 CST

I found a script for computing the angle between 2 vectors defined by atom centers using VMD on the AMBER mail reflector. I've been trying to modify it to compute the angle between 3 atoms. I keep getting this error:
 
Info) Segments: 1Info) Fragments: 34 Protein: 30 Nucleic: 0dcdplugin) detected standard 32-bit DCD file of native endiannessdcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)Info) Using plugin dcd for coordinates from file h5ltnw100.dcdInfo) Finished with coordinate file h5ltnw100.dcd.0380atomselect0atomselect1atomselect2can't read "1": no such variableInfo) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)Info) Exiting normally.
I commented out all the lines that contain a "1" , but I still get that error. Here's the script as
I last ran it:
 
#modified from script found in AMBER archive
# Monomer 1
set outfile [open atheta.txt w]
# load pdb file defining atoms & dcd file
mol load pdb tanw.pdb dcd h5ltnw100.dcd
set nf [molinfo top get numframes]
set pt1 [atomselect top "resid 1449 and name C2"]
set pt2 [atomselect top "resid 1448 and name C1"]
set pt3 [atomselect top "resid 1447 and name C1"]
#set conv [expr 180.0/acos(-1.0)]
#calculate first the 2 vectors v1 & v2 & their lengths v1l & v2l
#then the angle
#get the coords for 2 points
for {set i 0} {$i <$nf} {incr i} {
$pt1 frame $i
$pt2 frame $1
set coor1 [measure center $pt1]
set coor2 [measure center $pt2]
#do the first vector
set v1 [vecsub $coor1 $coor2]
set v1l [veclength $v1]
 
#get coords for next 2 points
$pt2 frame $i
$pt3 frame $i
set coor3 [measure center $pt2]
set coor4 [measure center $pt3]
#do 2nd vector
set v2 [vecsub $coor3 $coor4]
set v2l [veclength $v2]
 
#do dotproduct
set dotp [vecdot $v1 $v2]
#do angle
set theta [expr $conv * acos($dotp/($v1l*$v2l))]
#if {$theta > 90.0} {
# set theta [expr 180.0 -$theta]
#}
#puts $outfile "[expr($i+1)*10] $theta"
puts $outfile "$i $theta"
}
close $outfile
 
Thanks for any help!
 
Irene Newhouse
_________________________________________________________________
Connect and share in new ways with Windows Live.
http://www.windowslive.com/share.html?ocid=TXT_TAGHM_Wave2_sharelife_012008