AMBER Archive (2008)

Subject: Re: AMBER: bond breaking in proteins

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 26 2008 - 11:16:46 CST

On Tue, Feb 26, 2008, Eddie Mende wrote:
>
> I am trying to do bond breaking in a protein, the force field I am
> trying so far
> is the ff03. For the broken piece I get a QM part, and I am using options
> 1 and 3 in different runs to see how they behave.
> I started doing some standard MM simulations, and the protein looks good
> at various temperatures, however when I do QM/MM the bond breaks
> spontaneously hence I do not pursue the matter further, as I know my
> free energy calculations would be too off the mark.
> A reason for this may be that the AM1 Hamiltonian needs to be that
> of a closed shell structure, so when the pieces are separated this
> Hamiltonian
> may have some problems...etc. ( I am breaking a Histidine -Phosphate group)

I think you will need to be more specific in describing your problem:

a. What exactly is your quantum region? You talk about "closed-shell"
    structure, but it is not clear how this question is relevant.

b. You say "the bond breaks spontaneously", but we don't know which bond this
    is. What exactly do you mean by the term "broken pieces"?

c. You probably will need to actually post your input file, and describe in
    much more detail exactly what you are trying to do.

...dac

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