Re: Re:

From: Chris Harrison (
Date: Thu Aug 30 2012 - 03:25:09 CDT

> On Wed, Aug 29, 2012 at 9:06 AM, Jacqueline Schmidt
> <> wrote:
> (for instant in I want calculate
> average angle resulted for a particular bondangle etc), how should I
> actually do that.

TO Measure Angle:

This scripted VMD proc should get you started measuring angles and
outputting them to a file.
Usage: put the proc in a file (ie scanAngle.tcl) and load it into vmd through the TKConsole with "source scanAngle.tcl", then use with: "scanAngle $yourAtomSelection yourOutputFileName firstFrameToMeasure lastFrameToMeasure""

proc scanAngle {sel {outputFileName "angleScan.dat"} {startFrame 0}
{lastFrame 0} } {
  # Beware, there may be bugs. This proc was quickly written as an
  # example.
  if { [ llength [$sel get index ]] != 3 } {
    puts "Your atomselection must contain 3 particles, no more, no less"
  set fd [open $outputFileName "w"]
  set myMolid [ $sel molid ]
  if { lastFrame == 0 } {
    set lastFrame [ molinfo $myMolid get numframes ]
  for {set i startFrame} {$i<=$lastFrame} {incr i} {
    set myAngle [ measure angle [lindex [$sel get index]] frame $i molid $myMolid ]
    set myData "$i, $myAngle"
    puts $fd $myData
  close $fd

NOTE: You could also just tag/label the atoms and open the label
dialogue and then click on the "graph" tab.

> rama plots and so on) with my self-written

To Measure Ramachandran Plot:
Just use the VMD Plugin: Extensions > Analysis > Ramachandran Plot

> into the insight format (ASCII format) and do various analysis (density
> profiles of different groups,

You'll have to be little more specific about what you are trying to
calculate here.'

> My other question is about NAMDEnergy plugin. When I try to run it I get the
> error message that It can not execute the namd2 executable file! this is
> while I run my simulations with the same file (the namd2). Does anyone know
> why is this happening?

As someone said earlier; Norman, I think; VMD can find namd2. Add it to
your PATH.


Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078               Fax:   217-244-6078

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