AMBER Archive (2004)

Subject: AMBER: thermodynamic integration of ring opening

From: Carsten Detering (detering_at_u.washington.edu)
Date: Mon May 17 2004 - 15:37:42 CDT

Dear ambers,

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.

Thanks for helpful suggestions,

Carsten

--------------------------------------------
Carsten Detering
University of Washington
Department of Chemistry
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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