Re: [AMBER] About penalty scores

From: David A Case <>
Date: Tue, 24 Oct 2017 08:09:55 -0400

On Mon, Oct 23, 2017, Arun Srikanth wrote:
> I used parmchk2 to get the parameters for my molecule.
> But one of the dihedral parameters has a high penalty score.
> Is there any way to correct this
> cd-cc-os-cc 2 2.100 180.000 2.000 same as X
> -c2-os-X , penalty score=232.0

The high "penalty" means that the required parameter is not very close to
one that has been parameterized, and this indeed looks like an odd
combination. "Correccting" this would involve checking what the force field
predicts compared to quantum calculations (or to experimental data if you have
it.) Amber's "paramfit" program is one way to approach such comparisons, and
is generally pretty easy to use. Others on the list may have their own
favorite approaches, and are welcome to chime in here.


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Received on Tue Oct 24 2017 - 05:30:02 PDT
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