AMBER Archive (2004)

Subject: Re: AMBER: Assignment of parameters, missing parameters

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 23 2004 - 16:28:59 CST

On Mon, Mar 22, 2004, Julien Michel wrote:
>
> I would like to report that Leap can assigns torsions incorrectly when
> generating a prmtop file. The problem seems to be caused by atom typing.
> How is it possible to differentiate the following torsion ca-ca-ca-ca in a
> phenyl ring and ca-ca-ca-ca in a biphenyl(GAFF atom types) ?

This is one of the areas where the new gaff2 force field is an improvement
over that in Amber 7. As you note, the problem can be (mostly) solved
by introducing new atoms types, which has been done. The updated files should
be available soon at the Amber web site (go the "antechamber" link).

...good luck....dac 

-- 

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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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