Re: AMBER: RADII in DELPHI

From: David A. Case <case.scripps.edu>
Date: Thu, 17 Jul 2003 09:03:29 -0700

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 

-- 
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David A. Case                     |  e-mail:      case.scripps.edu
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Received on Thu Jul 17 2003 - 17:53:00 PDT
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