On 11/13/14 2:14 AM, md kashif wrote:
Dear all Can anyone suggest that how to compare change in energy of my protein before docking and after docking by a ligand. Please suggest any suitable tutorial or paper if possible.
You can easily calculate an energy value for the protein (single point energy calculation), but it's not a free energy and it's totally force field-dependent. Proteins are generally (mostly) rigid during docking, so any change in the energy is probably small.
If this is related to your previous posts about the energy value after minimization, it's really not a useful quantity because the systems are simply different.
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