On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
Dear all,
Why all people cut the protein ligand bond to produce the photodissociation?
Because MM forcefields typically assume bonds do not break or form.
Electronic degrees of freedom are not directly considered in the model.
For instances, In myoglobin, To simulate photodissociation of the CO
complex, the Fe–CO bond of the
starting structure was cut before any calculation.Fe-C bond were cut and
instantaneously switch the heme force
field from 6-coordinated Fe to that of the 5-coordinated Fe.
I want to understand how we can delete this bond between Fe-CO to induce
the photodisssociation ? After we cut the bond what it can do during MD
simulation ?
If you know enough about such a system to parametrize the bonded and
non-bonded systems, then in principle you could watch the process of
dissociation after cleavage. But I can imagine spending 6 months to do
that parameterization and still failing. A modelling approach that works
nicely for simple first- and second-row elements not undergoing chemical
reactions need not be extensible to either transition elements or reactions.
Mark
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