On Thu, Jul 17, 2003, Obdulia Rabal wrote:
>
> I don't know what RADII parametrization use in delphi:
>
> 1) RADII in prmtop by writing "set default PBradii pbamber"
These are experimental and have not yet been published (as far as I know),
so are probably not what you want.
> 2) radii extracted from a .crd by using ptraj
Also not what you want.
You should probably read papers about delphi use, and follow their lead, at
least as a first step. Most (but by no means all) calculations use Bondi
radii, or something pretty similar to that.
...dac
--
==================================================================
David A. Case | e-mail: case.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 Thu Jul 17 2003 - 17:53:00 PDT