When I'm preparing small ligand molecules, I closely follow tutorial 4b.
https://ambermd.org/tutorials/basic/tutorial4b/
Something described in the tutorial that is not present in your logs are the use of the saveoff and loadoff commands which read/write residue definitions for future use. I would recommend putting your system aside for the time being and instead work through this tutorial a few times.
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Received on Fri Jan 10 2025 - 06:30:02 PST
