I am working on a docking study of different antibiotics. I want to check the metal effect on the docking site or any active site in protein. So how can I add it with a ligand? Are there any docking tools are available for it?
This may depend on the tools you are using. Do you have the appropriate metal ion definitions within your 'forcefield' model? You could consider using a tool such as MOPAC (http://openmopac.net/) to model the site and ligand with the metal ion in place.
Dear Darshan,
The best method to be used is running a DFT calculations on the ligand attached to the metal ion, then you take the global minimum structure obtained from the DFT calculations and conduct the docking.
Semi-empirical methods are inadequate since they do not handle metal ions.
DFT installed in Gaussian can be a good choice to achieve your goal.
Good luck,
Rafik
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