Hi,
If you're looking for hydrogen bonds between to molecules, make sure
you use the 'nointramol' keyword so you ignore intramolecular hydrogen
bonds.
You may also find the basic hydrogen bond analysis tutorial with
cpptraj useful:
http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/
Hope this helps,
-Dan
On Wed, Aug 22, 2018 at 4:15 AM Meng Wu <wumeng.shanghaitech.edu.cn> 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 Aug 30 2018 - 07:00:02 PDT
