VMD-L Mailing List

From: Payne, Christy (Christy.Payne_at_nrel.gov)
Date: Tue Jul 12 2011 - 10:31:26 CDT

Bernard,

This script will work to get you the pucker parameters using the "get pucker" command.

proc hrpucker {selection} {
        # some error checking
    if {[$selection num] <= 0} {
                error "hrpucker: needs a selection with atoms"
    }

    # save the selection frame number and get the molecule id.
    set sel_frame [$selection frame]
    set gr_mol [$selection molindex]

    # open a file for the output
    set filename "pucker.txt"
    set outfile [open $filename w]

    # make a list of pucker parameters
    set num_frames [molinfo $gr_mol get numframes]
    for {set i 0} {$i < $num_frames} {incr i} {
        $selection frame $i
        # get pucker parameter and save it on the list
        set pucker_parm [$selection get pucker]
        puts $outfile "$i $pucker_parm"
    }

    close $outfile
   return
}

Christy

On 7/12/11 8:03 AM, "Axel Kohlmeyer" <akohlmey_at_gmail.com> wrote:

bernard,

On Tue, Jul 12, 2011 at 8:40 AM, Mr Bernard Ramos <bgrquantum_at_yahoo.com> wrote:
Hi Dr. Stone!
I corresponded with Dr. Michelle Kuttel regarding obtaining Cremer-Pople (CP) ring puckering parameters in VMD. Dr. Kuttel gave me your email address for this concern.

I am new to VMD and I am using VMD 1.8.7. I need to have the three CP parameters for each frame in my trajectory file. A simple lists for each ring in each frame will be fine for me. I hope you can help me with this.

you should two three things:

- upgrade to VMD 1.9

- familiarize yourself with VMD/Tcl scripting for analysis
  and particularly how to use the atomselect command.
  (there is a special section for that in the user's guide
  and there are tutorials; you may also need to have a
  look at the tcl tutorial at www.tcl.tk <http://www.tcl.tk> ).

- write a suitable analysis script that defines an atom
  selection for your atoms of interest and then use the
  (undocumented?) "pucker" property to retrieve the
  information you desire.

i strongly suggest to do these things in order and
don't rush the middle step.

axel.

Thanks,

Bernard