[Dock-fans] Doubt about Zinc based active sites

Arvind Ramanathan rarvind at cs.sunysb.edu
Fri Jul 8 07:16:07 PDT 2005


Hi,

As I was trying to dock a molecule into thermolysin, I observed that it
was not docking correctly to the protein. Hence, I looked at the various
steps, and found that when grid is run, I get the following output (in
verbose mode):
Chemical Assignment
  4698    C   C.2   null
  4699    O O.co2   acceptor
  4700  OXT O.co2   acceptor
  4701  ZNA    Zn   null

Shouldn't Zinc have some information about this? I thought it was a donor.
How do I incorporate this information into the tables. Is there any way I
can do this?

  4698    C   C.2 Carbon_sp/sp2        1 19
  4699    O O.co2 Oxygen_Sp2           1 17
  4700  OXT O.co2 Oxygen_Sp2           1 17
  4701  ZNA    Zn null                 0 0

Shouldn't Zinc have some type associated with it or some VDW parameters
associated with it?

Your help will be sincerely appreciated.

Thanks,
Arvind



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