Re: [AMBER] CPPTRAJ, Total H-Bond Count Question

From: Daniel Roe via AMBER <>
Date: Fri, 24 Jun 2022 14:51:23 -0400


On Mon, Jun 20, 2022 at 8:23 AM Matthew Guberman-Pfeffer via AMBER
<> wrote:
> 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.)

Make sure that the angle cutoff in particular is the same; cpptraj and
VMD defines the cutoffs differently. A valid hydrogen bond for cpptraj
has a D-H-A angle greater than the cutoff (default 135). In VMD it's
*deviation* from linear (180 deg.), so the cpptraj default of 135 is
45 for VMD.

Does that make sense?


> Any insight would be much appreciated.
> Best,
> Matthew
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Received on Thu Aug 04 2022 - 13:33:10 PDT
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