AMBER Archive (2004)

Subject: Re: AMBER: thermodynamic integration of ring opening

From: David A. Case (
Date: Mon May 17 2004 - 18:21:15 CDT

On Mon, May 17, 2004, Carsten Detering wrote:
> 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.

Generally, a dummy atom keeps the bond and angle terms that it had as a "real"
atom, while that dihedral, vdW and charge terms are all set to zero. The
bond and angle terms keep the dummy atom near to the positions they have in
the real system, and hence generally enhances sampling.

good luck...dac

[p.s. the question I always have about your mutation is: what is the
environment of the indole nitrogen in the lambda=1 state? This is not
something that I need to know.... It just sounds like you are taking an
8-electron system (CH2) into a one-electron system (H).]
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