AMBER Archive (2005)

Subject: Re: AMBER: bond type for a virtual bond in a biomolecular transition state

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 02 2005 - 17:08:38 CST

On Wed, Mar 02, 2005, Eric Hu wrote:

> I am building a frcmod file for a transition state of a
> bimolecular reaction.

I don't have an answer to your particular question, but I hope you realize
that what you are trying to do is unlikely to work. The way in which
antechamber figures out bonding rules is based on how stable, closed-shell
ground-state molecules behave. You should not expect that the bond types,
charges, or force field parameters would work for a transition state.

If you are making your own force field parameters, then please realize that
the Amber energy function has no notion of a "bond type". Bonds are bonds,
and are not classified any further. (Internally, antechamber uses some bond
types for a couple of types of classification; you can read about these
at http://amber.scripps.edu/antechamber/antechamber.pdf.)

...hope this helps...dac

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