[AMBER] Hydrogen Bonding Analysis

From: Huimin Tian <201921150072.mail.bnu.edu.cn>
Date: Mon, 20 Dec 2021 17:27:40 +0800 (GMT+08:00)

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,

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Received on Mon Dec 20 2021 - 01:30:01 PST
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