AMBER Archive (2004)

Subject: Re: AMBER: thermodynamic integration of ring opening

From: Bill Ross (
Date: Mon May 17 2004 - 17:47:24 CDT

> I am asking again about the TI of the opening of a ring.
> I have a 2-Methyl-2,3Dihydro-isoindol-1-one system. I would like to mutate
> the C3 atom (opposite to the keto group in the 5-membered ring) into an H
> which is bound to the C-atom next to it in the six-membered ring.
> The two hydrogens become dummy atoms, and the ca to which they are bound to
> is mutated into an ha. How do I tell leap now that the ha is not bonded to
> the nitrogen? When I check the molecule in leap, I need to specify the bond
> and angle parameters, but since there is no bond, I cannot specify them.
The programmatic reality is that your ha remains bonded to
the nitrogen. Therefore you need to choose a novel atom
type for the new hydrogen and assign it parameters that
are correct on the bonded side and 0 on the disappeared-
bond side. If the parameters on the two sides overlap,
you will need to change the type of one of the atoms it
is bonded to to another novel type and replicate the
parameters for that type.

Experts may have better advice.

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