Dear Amber Community,
I performed an aMD simulation of a fairly large protein complex, and I only now noticed the comment in the tutorial "For larger proteins with more than 100 residues, the energetic noise would be too high for accurate reweighting” (
https://mccammon.ucsd.edu/computing/amdReweighting/ <
https://mccammon.ucsd.edu/computing/amdReweighting/>). I wanted to run MM-GBSA on snapshots from the aMD simulation to assess the binding interaction of the protein domains, but I’m not sure if or how the results should be re-weighted. I’d greatly appreciate any suggestions.
Best regards,
Matthew
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Received on Tue Jul 13 2021 - 06:00:02 PDT
