AMBER Archive (2005)

Subject: Re: AMBER: ambpdb radii

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 25 2005 - 12:15:57 CST

On Fri, Feb 25, 2005, Harianto wrote:

> Of course I did. Assuming I cannot read fortran, there is ref:
> from Sitkoff, Sharp & Honig, PARSE values, J. Phys. Chem. 98:1978(1994).
> So from this the radii come, right?

Sorry...I didn't realize you could not read code. A "C" in column 1 in
Fortran means a comment line, which is ignored by the compiler. Hence, the
reference you want is:

c Bondi radii, from Huheey, Inorganic Chemistry: Principles of Structure
c and Reactivity, 2nd ed. p. 232.

If you look at the radii in the pqr file, it should be clear what you are
getting, and you can decide if it meets your needs or not. There is nothing
magic or special about the radii the ambpdb uses.

...dac

The "original" reference is

%A A. Bondi
%J J. Chem. Phys.
%V 64
%P 441
%D 1964

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