VMD-L Mailing List

From: jo hanna (jfhanna_at_gmail.com)
Date: Fri Sep 07 2007 - 17:18:33 CDT

Hi

I am trying to calculate the angle between specific atoms in my files (pdb
and xtc) at each frame. The script I'm using is as follows:

**

set outfile [open angle.dat w]
set frame0 [atomselect top "all within 3 of index 2" frame 0]
set nf [molinfo top get numframes]
for {set i 0} {$i<$nf} {incr i} {
  set A [atomselect top "index 2" frame $i]
  set B [atomselect top "index 0" frame $i]
  set C [atomselect top "index 1" frame $i]

  global M_PI

  # initialize arrays
  set a() 0; set b() 0; set c() 0; set ab() 0; set ac() 0;

  # split coordinates
  set a(x) [lindex $A 0]; set a(y) [lindex $A 1]; set a(z) [lindex $A 2];
  set b(x) [lindex $B 0]; set b(y) [lindex $B 1]; set b(z) [lindex $B 2];
  set c(x) [lindex $C 0]; set c(y) [lindex $C 1]; set c(z) [lindex $C 2];

  # setup vectors
  set ab(x) [expr $b(x) - $a(x)];
  set ab(y) [expr $b(y) - $a(y)];
  set ab(z) [expr $b(z) - $a(z)];

  set ac(x) [expr $c(x) - $a(x)];
  set ac(y) [expr $c(y) - $a(y)];
  set ac(z) [expr $c(z) - $a(z)];

  # compute cosine
  set cosine [expr \
    ($ab(x)*$ac(x) + $ab(y)*$ac(y) + $ab(z)*$ac(z)) / \
    (sqrt(pow($ab(x),2) + pow($ab(y),2) + pow($ab(z),2)) * \
     sqrt(pow($ac(x),2) + pow($ac(y),2) + pow($ac(z),2)))];

puts $outfile "set angle [expr acos($cosine)*(180.0/$M_PI)]"
}
close $outfile

**

Using this gives me an error that I don't understand and therefore can't
fix:

syntax error in expression "atomselect10 - atomselect9": variable references
resuire preceeding $

Can someone please advise?

Thanks
Jo