AMBER Archive (2004)

Subject: Re: AMBER: Molecular Frame

From: David A. Case (case_at_scripps.edu)
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
this.

.good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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