AMBER Archive (2003)

Subject: Re: AMBER: RADII in DELPHI

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 17 2003 - 11:03:29 CDT

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_at_scripps.edu
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