AMBER Archive (2004)

Subject: Re: AMBER: generalized Born parameters

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 08 2004 - 11:08:02 CDT

On Fri, Oct 08, 2004, Peter Varnai wrote:
>
> According to the manual igb=2/5 parameters "are recommended for most
> projects" - is this true for nucleic acids as well? I would welcome
> pointers to published papers or other experience that demonstrates this
> statement for nucleic acids.
>

We are now running some side-by-side comparisons of various igb values for
DNA duplexes, but have not yet analyzed the reults. I don't know of any other
work along these lines. So, as far as nucleic acids are concerned, the
recommendation quoted above is only based on general principles, not on any
concrete evidence. (Alexey Onufriev may know more....)

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu