[AMBER] CPPTRAJ, how to write first solvent shell trajectory

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Sat, 9 Apr 2022 05:59:05 -0400

Dear Amber community,

I want to write a trajectory where I only retain the WAT and Na+ residues within the first salvation shell.
I’ve used the watershell command in CPPTRAJ to figure out that there are 3412 :WAT or :Na+ molecules within 3.4 Å on average.
I then tried to use the solvent command and the closest command, but it complained that the solvent (defined as :WAT,Na+) was not all of the same size.
I’m now thinking of directly using the strip command, but my understanding is that it will not update a distance-based selection for the solvent on each new frame. Is that right?
How can I write a trajectory that retains only the waters and Na+ ions within the first salvation shell?

Best,
Matthew


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Received on Sat Apr 09 2022 - 03:00:02 PDT