[AMBER] How to characterize Binding Sites with cpptraj

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From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Wed, 13 Oct 2021 14:07:47 -0400

Dear Amber Community,

I had the thought that it would be nice to quickly quantify the number of non-polar, polar, aromatic, basic, acidic, etc. residues in a binding site, either absolutely or as a fraction of the total number of residues within a certain distance. Is there a way to conveniently do this in cpptraj? If not, perhaps it could be a new feature?

Best,
Matthew
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Received on Wed Oct 13 2021 - 11:30:02 PDT