AMBER Archive (2006)

Subject: RE: AMBER: angle between two vectors. .

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Mon Oct 16 2006 - 15:51:28 CDT

Hi,
   Thank you very much to all who have responded.
Thanks,
ThuZar

You can use tcl script in VMD.
You may want to modify the following tcl script.
Enjoy it.

+++++++++++++++++++++++++++++++++++++++
set outfile [open cn-m2-vmd.dat w]
set nf [molinfo top get numframes]
set g34 [atomselect top "resname GLY and name CA"]
set v27 [atomselect top "resid 7 34 61 88 and name CA"]
set c5 [atomselect top "resname HMT and name C5"]
set n1 [atomselect top "resname HMT and name N1"]
set all [atomselect top all]
set conv [expr 180.0/acos(-1.0)]

# angle calculation loop
for { set i 0 } { $i < $nf } { incr i } {
  $g34 frame $i
  $v27 frame $i
  set com1 [measure center $g34]
  set com2 [measure center $v27]
  set m2 [vecsub $com2 $com1]
  set m2mag [veclength $m2]

  $c5 frame $i
  $n1 frame $i
  set com3 [measure center $c5]
  set com4 [measure center $n1]
  set cn [vecsub $com4 $com3]
  set cnmag [veclength $cn]

  set dotp [vecdot $m2 $cn]
  set theta [expr $conv * acos($dotp / ($m2mag * $cnmag))]
  if { $theta > 90.0 } {
    set theta [expr 180.0 - $theta]
  }
  puts $outfile "[expr ($i + 1) * 10] $theta"
}
close $outfile
++++++++++++++++++++++++++++++++++++++++++

On 10/12/06, David A. Case <case_at_scripps.edu> wrote:
> On Thu, Oct 12, 2006, Lwin, ThuZar wrote:
>
> > Do you have any suggestion on how to do the following using
amber
> > ptraj?
> > Vector 1: Assign a vector between atom A and B.
> > Vector 2: Assign another vector between atom C and D.
> > Then calculate angle between vector 1 and vector 2.
>
> My best guess is to use the vector command to write out files with the
two
> vectors as a function of time, then use a short awk or perl script to
compute
> the angles.
>
> (This would be a good functionality to have inside ptraj, but as far
as I
> know, it is not there now.)
>

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