AMBER Archive (2005)

Subject: Re: AMBER: parameters in gaff.dat

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 15 2005 - 01:02:48 CDT

On Fri, Apr 15, 2005, Lihua Wang wrote:
>
>
> 2. If two atom types are 'identical' as indicated in gaff.dat, can i
> suppose that they are interchangeable? if they are truly identical, why
> are some parameters that are supposed to be 'identical' vastly different?
> For example:
>
> nd-cc-nh are nc-cd-nh are 72.4 120.11 while
> nc-cc-hn and nd-cd-nh are 73.9 111.94

Since, as you point out, the parameters are quite different, I don't
understand why you are convinced that the atom types themselves are
"identical".

In any event, the rationale and use of cc/cd pairs (and others like that)
is explained in detail here:

%A J. Wang
%A R.M. Wolf
%A J.W. Caldwell
%A P.A. Kollman
%A D.A. Case
%T Development and testing of a general Amber force field
%J J. Comput. Chem.
%V 25
%P 1157-1174
%D 2004

....dac

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