Hi,
Please see the 'hbond' command entry in the Amber (or cpptraj) manual.
You need to specify the 'solventdonor' and/or 'solventacceptor'
keywords (and potentially other output-related keywords like
'solvout') to calculate solute/solvent hydrogen bonds. I recommend
reading the entire manual entry.
Good luck,
-Dan
On Mon, Dec 20, 2021 at 4:28 AM Huimin Tian
<201921150072.mail.bnu.edu.cn> wrote:
>
> Dear all,
> I have encountered a problem when I use cpptraj to monitor the presence of hydrogen bonds during our trajectory.
> Here is the cpptraj script that we will use:
> trajin heat.binpos
> hbond :* avgout avg-hbt.dat printatomnum
> :* means "consider all residues in the analysis."
>
> avgout avg-hbt.dat "tells cpptraj to print out the solute-solute hydrogen bond averages to file."
> printatomnum "tells cpptraj to include atom numbers in the output."
> So, there are only hydrogen bonds between residues in hydrogen bond analysis.
> Cpptraj does not show the hydrogen bond between the residue and water. What is the reason?
> What can be done to show the hydrogen bond between the residue and the water molecule?
> Does it make sense to analyze the hydrogen bonds between residues and water molecules?
>
>
>
> Thanks and Regards,
> Tian
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 20 2021 - 07:00:02 PST
