[AMBER] CPPTRAJ, Total H-Bond Count Question

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Sun, 19 Jun 2022 17:11:38 -0400

Dear Amber Community,

CPPTRAJ hbond keyword gives me a total solute-solute H-bond count in All.hbvtime.dat of 242, which is surprisingly small for my structure.
How is the total determined? If multiple H-bonds exist between two residues, are they counted as one H-bond?

I’m trying to understand why the number is so small. If I run the H-bond analysis in VMD, I find ~2000 unique H-bonds. (I made sure to adjust the distance and angle criteria in CPPTRAJ and VMD to be the same for this comparison.)

Any insight would be much appreciated.


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Received on Thu Aug 04 2022 - 13:32:20 PDT
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