AMBER Archive (2008)

Subject: AMBER: bond breaking in proteins

From: Eddie Mende (pckboy_at_gmail.com)
Date: Tue Feb 26 2008 - 10:16:21 CST

Hello

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)

My question is: Should I try a different force field (say ff02 I
think,..the one with dipoles),
and for the QM part, what solutions would be most fit?.

Shall I try explicit water?. Should I try doing QM water, and may be
hold some waters
with a soft potential fixed around the Nitrogen of the Histidine?.
Waters may help
to balance the charge between broken pieces.

Please let me know what you all think

Thanks

Eduardo Mendez
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