AMBER Archive (2004)

Subject: Re: AMBER: Molecular Frame

From: David A. Case (
Date: Sat Jan 03 2004 - 09:51:13 CST

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