Re: AMBER: Molecular Frame

From: David A. Case <>
Date: Sat, 3 Jan 2004 07:51:13 -0800

On Fri, Jan 02, 2004, Byungchan Kim wrote:

> I want to calculate order parameter (S2) of backbone N-H.
> To calculate rotation correlation function of N-H bond vector,
> I need to calculate the bond vector respect to molecular frame.
> Is there any pre-set way or program to do this easily?

The "rms" and "correlation" commands in ptraj are designed to do exactly

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jan 14 2004 - 15:53:13 PST
Custom Search