Subject: Re: Amber's new parameters

From: <[email-masked]>
Date: Tue, 23 May 1995 22:59:18 -0700

I just read in the latest JACS issue (JACS 1995, 117, 5179-5197)
	a VERY interesting article about the developing of new parameters for
	the simulation of proteins and nucleic acids ...

	It is also mention here a WWW site where those parameters can be 
	found and downloaded. These parameters ar for AMBER.

The parameters will soon be on http://www.amber.ucsf.edu/amber/amber.html
(sometime on Wednesday, I expect). There are already some writeups there
on practical considerations in developing compatible parameters.

	1) What does exactly AMBER do? (strong and weak points).

Aside from the force field, there is a program package called
AMBER. Both are described on the web pages.

	2) Is AMBER available for PCs? if so, under what Operating System?

It has been compiled using f2c-based f77 under linux and 
bsd on PCs. Using Unix, one can generate source for e.g. 
DOS for use with a DOS fortran compiler. My guess is that
using a fortran compiler rather than f2c/f77 (which uses
C-translated source) gives a speedup of about 2x. AMBER
has most commonly been run on workstations & supercomputers,
but now that PCs have gotten faster, this contingent is
growing.

	3) Who distributes AMBER? Latest Version? Price? 

University of California, San Francisco and Oxford Molecular.
Latest version is 4.1, academic price is $200. Contact info
is on the web pages; briefly for those w/out web access:

UCSF	
	[email-masked]  	(also for joining the amber mail
					reflector)

Oxford Molecular

	USA  	[email-masked]
	UK	[email-masked]
	France	[email-masked]
	Germany	[email-masked]

Bill Ross