Every thing that changes MUST be in the perturbed group.
The general advice for running Gibbs it to have ALL interactions
turned on.
On Fri, 14 Mar 2003, Ghislain Deslongchamps wrote:
> Hi folks,
>
> Using AMBER 7/GIBBS, we are mutating a phenol group (Ar-O-H) into a benzene
> (Ar-H-Du, Du=dummy) in a 54-carbon molecule using electrostatic decoupling.
> RESP charges were calculated for both molecules. Since the RESP charges are
> different for all atoms on both structures, is GIBBS flagging all the atoms
> as part of the intra-perturbed group? Our FEP results gave erroneous
> electrostatic energy terms unless intra-perturbed group interactions were
> omitted (INTPRT=0).
>
> Should this resolve itself if we use the same RESP charges on all atoms on
> both molecules except those directly involved in the mutation?
>
> Any help will be gratefully appreciated,
>
> -Ghislain
>
> -----------------------------------------------------------
> Dr. Ghislain Deslongchamps, Professor
> Director of Undergraduate Studies
> Department of Chemistry, Faculty of Science
> University of New Brunswick
> Fredericton, N.B. CANADA E3B 6E2
> phone: (506) 453-4795 cell: 451-5166 FAX: 453-4981
> e-mail: ghislain.unb.ca WWW: http://biocomp.chem.unb.ca
> -----------------------------------------------------------
>
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Received on Fri Mar 14 2003 - 15:53:02 PST
