AMBER Archive (2008)

Subject: Re: AMBER: united atom force field: antechamber

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 19 2008 - 17:33:32 CST

On Tue, Feb 19, 2008, fatima.chami_at_durham.ac.uk wrote:
>
> I have used Antechamber to generate topology file for my molecule using GAFF
> Is it possible to translate this into a united atom force field using ff03ua
> through antechamber.

No: gaff is intrinsically an all-atom model. The united-atom parameters for
proteins were developed "by hand", and I don't think there is any general
prescription for how to do something similar for arbitrary molecules.

[You should be careful what you wish for....do you have a *real* need for
a united atom ligand? There were some good reasons why united atom force
fields mostly disappeared from biomolecular MM simulations a quarter of a
century ago. It would be a shame if people had to re-discover the limitations
of the UA scheme all over again.]

....dac

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