From: Payne, Christy (Christy.Payne_at_nrel.gov)
Date: Thu Jul 07 2011 - 14:35:18 CDT

I have written a VMD tcl script to obtain the pucker parameters for a six-member ring over the course of a trajectory. I have a couple of questions regarding what I get back.

 1. Are these parameters still obtained using the Hill-Reilly methodology? [using $sel get pucker]
 2. How are the three Hill-Reilly angles describing canonical ring pucker conformations combined to obtain a single parameter?

Thanks!
Christy