I want to run docking involving mercury metal ion can anyone suggest me which software support or have mercury parameters for efficient docking results.
For AutoDock, you might find some suggestions in this thread:
http://mgldev.scripps.edu/pipermail/autodock/2012-June/008283.html
In general, there are two ways:
1. Approximation: Replace "mercury" atom in the model with another atom (already present in the force field) with similar properties to "mercury". This is a "quick & dirty" approach but might be sufficient.
2. Modification of the force field: Add parameters for "mercury".
Dear Martin,
Can you please guide me how can I get parameters for mercury or how to generate those parameters????
Have you tried the approximation approach? The parameters for zinc are included in Autodock.
If you want to add mercury explicitly, here is the list of parameters that you need to define:
http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4/?searchterm=force%20field
. . . and if you look here:
http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters
. . . you can use zinc as the template and adjust the "Rii", "epsii", and "vol" parameters to "match" mercury. You can find the parameters in literature.
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