Article ID: 115 - Last Modified: December 4, 2010
My QSite calculations are running for a long time and are not converging. What can I do?
If you are using an implicit solvent model, this could be the problem. We don't recommend using continuum solvation when modeling buried active sites. The interaction with the solvent would be confined to the periphery of the protein, but that region is far from the active site and therefore not so important. It is probably better to freeze the periphery of the protein and let the interior relax. If solvation of the protein so far away from the active site is actually believed to be important for how the active site behaves, then an alternative is to use explicit solvation using Soak, and then freeze at least the water molecules' positions.
Keywords: Qsite, implicit solvent, PB, explicit solvation, convergence issue
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