Subject: Re: CCL:residue cross correlation

From: Anton Feenstra <feenstra(at)chem.vu.nl>
Date: Mon, 19 Jan 2004 07:58:40 +0100

Bimo Ario Tejo wrote:

> Dear all,
> 
> I'm just wondering does anyone have a program to calculate residue
> cross-correlation (DCCM) of MD trajectories based on vectors (origin at mean atom
> position during simulation)? I need such a program that able to read any
> trajectories regardless what program used (CHARMM, Amber, Gromacs, etc.)...

AFAIK, there is no common trajectory format, not even one that is recognized
by more than a few programs... ;-{
What I do know, is that most programs can write pdb files, and also most
can read them again. Gromacs can recognize concatenated pdb files as a
trajectory, and can read and write it as a native format (although slower
than most other formats, and huge amounts of diskspace...) I'm not sure
which correlations you mean, but I'm pretty sure it is possible to calculate
them with one of the many analysis tools of Gromacs.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra(at)chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|

---

From: Richard Wood <rlw28*at*cornell.edu>
Date: Mon, 19 Jan 2004 11:24:33 -0600

Hi all

If one used CHARMm/CHARMM to calculate these trajectories, why can't one 
use CHARMm/CHARMM to analyse them?

Richard