Dear AMBER Community,
Background: I want to generate possible configurations for a homodimeric complex of a ~100-residue, well-structured protein. My interest is in evaluating the inter-protein electron transfer rate within the configurations for the complex.
Question: I’d greatly appreciate suggestions on how to generate an ensemble of likely complexes? Is rigid-body Brownian dynamics possible in AMBER? Should I use protein-protein Gaussian Accelerated MD? etc.
Best,
Matthew
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Received on Fri Mar 22 2024 - 06:00:02 PDT
