Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj

From: Gustaf Olsson <>
Date: Thu, 13 Sep 2018 06:16:14 +0000

I provided one of my input files for HBOND analysis a few months ago, both for occupancy and lifetime analysis.

You can find it in the list archive:

Hope that helps!

// Gustaf

> On 13 Sep 2018, at 03:30, Meng Wu <> wrote:
> Deal amber users,
> I am going to make the H-bond analysis between the substrate molecule--acetates and the channel protein during the MD process in which substrate molecules pass through. I have read the 'hbond' command in Amber16 manual but still have no idea, could anybody give some guidance ? Thank you in advance!
> Best regards,
> Vector
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Received on Wed Sep 12 2018 - 23:30:01 PDT
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