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

From: Daniel Roe <>
Date: Thu, 13 Sep 2018 09:09:18 -0400


A good first pass is probably something like:

parm myparm.parm7
hbond H1 nointramol out nhb.dat avgout hbavg.dat

See the manual for full details on what each command and keyword is
doing. You may also find this tutorial useful:

Hope this helps,

On Wed, Sep 12, 2018 at 9:31 PM 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 Thu Sep 13 2018 - 06:30:03 PDT
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