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Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled challenges in a similar protein-ligand system?

Additionally, I'd appreciate insights on recommended approaches for addressing specific challenges and optimizing the simulation setup. The ultimate goal is to ensure that MD simulations precisely capture the nuances of protein-ligand interactions while maintaining computational efficiency.

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    $\begingroup$ It's a bit open-ended, but it should be fine. I'm not sure there are many experts on the topic her, so maybe transfer to Matter Modeling would be better. Please do not repost the question there without deleting it here first. Alternatively, raise a flag and we'll migrate it. $\endgroup$
    – Martin - マーチン ♦
    Commented Nov 18, 2023 at 13:00
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    $\begingroup$ Also see the AMBER Mail Reflector, which is quite active and very likely has addressed your question at some time. $\endgroup$
    – Todd Minehardt
    Commented Nov 18, 2023 at 14:16

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