Subject: BIOSYM vib. freq.

From: Ramon Garduno <[email-masked]>
Date: Fri, 24 Oct 97 20:49:34 CDT

Hello fellows!,

I need a prompt answer to the following. I am using DISCOVER, a part
of the BIOSYM suite of programs (now own by MSI), and while running an
MD run for a large protein molecule I am studying, I have the need 
of calculating the vibrational frecuencies for a large portion of this
molecule.

DISCOVER manual clearly states that the vibrational command in the DSL
Standalone mode will only do its task for small molecules or small
subsystems. As well, it says that part of the output will be funneled to
a vibrational frecuencies and eigenvectors file (*.frq).

Now, I wonder
1) if the file *.frq contains the information for all atoms in the molecule,
or just part of it, 
2) if the answer to (1) is "all atoms", where I can find a nice program to
give the information I need?. If answer to (1) is "part of the molecule", 
how big is it?, because maybe I am knocking at the wrong door, and
3) Can any body hint where I can find papers that will illustrate me
more in the subject of how to calculate vib. freq. from an MD run?.

Much obliged,

--

____________________________________________________________________________
		  	 Dr. Ramon Garduno-Juarez
                     Research Professor in Biophysics
INSTITUTO DE FISICA                  |  EMAIL:  [email-masked]
UNIVERSIDAD NAL. AUTONOMA DE MEXICO  |          [email-masked]
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Apdo. Postal 48-3                    |          (73)111611 & 175388
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