Hi,
A good first pass is probably something like:
parm myparm.parm7
trajin mytraj.nc
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:
http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/
Hope this helps,
-Dan
On Wed, Sep 12, 2018 at 9:31 PM 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 Sep 13 2018 - 06:30:03 PDT
