Dear AMBER users,
I hope you are all well. I would like to prepare a reduced system for
production MD that contains only my DNA duplex, all ions, and the nearest
100 water molecules that are closest to my DNA at the end of equilibration.
Could someone please help me with what is the best way to extract these 100
closest water molecules using cpptraj or another tool?
Best regards ,
Manu
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Received on Sat Jul 05 2025 - 04:00:02 PDT
