AMBER Archive (2006)

Subject: Re: AMBER: igb=2 and "bad atom type" conflict

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 07 2006 - 16:42:09 CDT

On Thu, Jul 06, 2006, Evan Kelly wrote:

> As per the discussion that Scott and I have been having (see below),
> can anyone elaborate on the meanings of the parameters x(l170-1+i), x
> (l175-1+i), etc. in mdread.f? In particular, I am looking to modify
> the code to handle Fluorine.

See the LCPO paper:

%A J. Weiser
%A P.S. Shenkin
%A W.C. Still
%T Approximate Atomic Surfaces from Linear Combinations of Pairwise
Overlaps (LCPO)
%J J. Comput. Chem.
%V 20
%P 217-230
%D 1999

Unfortunately, as far as I know, no parameters are available for halogens.

Someone needs to either do this, and/or contribute a better surface area
module for Amber.

...dac

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