Regarding MD simulation, a full description of the algorithm and method has to be provided including 1) Algorithm used to treat the non-bonding interaction. Please specify: the force fields used to treat the ligand as well as the receptor.Was the used FF able to reproduce structural parameters? 2) MD data should be analyzed in the context of water entering the binding site. If water enters, it should be included in energy calculations as it can decrease substantially the binding energy and change the conclusion substantially.
- Badges
- Science topic
- Similar topics
- Correction
More Rahul Jawarkar's questions See All
Similar questions and discussions