On Wed, Jul 24, 2002, Pascal Bonnet wrote:
>
> In GAFF (general amber force field) the carbon radius is 1.7 A and in
> parm99 is 1.9080 A (and 1.5 and ~1.7 for oxygen radius)
> I don't think it is coherent to use two different force fields in the
> same system receptor-ligand?
>
> Why in GAFF, the hydrogen radius of TIP3P model is 1.2 and not 0 as in
> parm9X?
> RADIUS HW 1.2 (from GAFF)
> HW 0.0000 (from pam99)
>
It looks like you are confusing the radius used for generalized Born
calculations with the Lennard Jones r-sub-e values, (although I can't
figure out what files you are getting your information from...)
In both parm99.dat and gaff.dat, carbons typically have an r-sub-e value
of 1.908, and the tip3p water hydrogen (which is called "HW" in parm99.dat
and "hw" in gaff.dat) is zero.
The values of 1.7 for Carbon and 1.2 for Hydrogen look like the "bondi radii"
that are used (in both force fields) for electrostatic radii in the
generalized Born solvation model. Unlike some other implementations of
continuum models, there is no requirement or expectation in Amber that the
"dielectric radii" used in GB should be the same as the r-sub-e values from
the Lennard-Jones terms.
So, the force fields are equivalent in this sense. Note also that all
atom types in gaff.dat are lower case, so the statement:
> RADIUS HW 1.2 (from GAFF)
must be wrong, since gaff doesn't have any atom type "HW".
..hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Jul 24 2002 - 08:13:48 PDT
