AMBER Archive (2003)

Subject: Re: atomic positional fluctuation

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu May 15 2003 - 15:38:07 CDT

"pengyo_at_rwja.umdnj.edu" wrote:
>
> Hi, Dear AMBER users:
> I want to calculate the atomic positional fluctuation for the MD
> trajectory file with carnal. But I couldn't find the keywords from the
> manual (AMBER 7.0). Could anybody please give me an sample input file or
> any links?
> Thanks in advance!
> Youyi Peng
>

Use ptraj instead. The keyword is "atomicfluct"; superimpose the
structures onto a reference structure prior by using "rms".

Best regards

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++