VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 12 2011 - 09:03:56 CDT

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).

- 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
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.