Dear AmberUsers,
I am naive in the modeling tools and please excuse me for this.
I am doing a simulation of a metalloprotein. I am using MCPB for metal site
parameterization. I need some clarification on the cluster charges assigned
to the active center for charge calculation using gaussian (large model in
MCPB).
In both the tutorial as well as the example, 0 charge is assigned to the
cluster containing the metal ion and the bound residues and their
respective capping. Considering that the metal ion has +2 charge and all
the residues with their capping are neutral, shouldn't the cluster charge
be equal to +2 rather than 0. Can anyone please clarify on this.
Thanks and Regards
Soma
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Received on Mon Jan 09 2012 - 01:30:03 PST
