On Sat, Jul 05, 2025, MAMTA YADAV via AMBER wrote:
>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?
The "closest" command in cpptraj should do what you describe. Type "help
closest" at the cpptraj prompt, or look in the Reference Manual.
...good luck...dac
p.s. However! What you describe for use in "production MD" sounds rather
dangerous. Why do you want only 100 waters? You will have ions with no
coordinating waters, plus way too few waters to solvate even a tiny piece of
DNA duplex.
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Received on Sun Jul 06 2025 - 11:30:03 PDT
