Hi,
Sorry for the delay in responding.
On Mon, Dec 20, 2021 at 9:25 PM Huimin Tian
<201921150072.mail.bnu.edu.cn> wrote:
> Does it make sense to analyze the hydrogen bonds between residues and water molecule?
Your question is pretty broad and depends on what you're researching,
but in general I believe it makes sense to study solute-solvent
hydrogen bonds. Water typically makes up the majority of your system,
and how it interacts with the solvent often has important effects on
structure/dynamics. In particular, "bridging" waters (i.e. waters
bonded to 2 or more solute residues) often have a large impact on
solute structure. Water-based analyses such as GIST/SPAM can then help
tease out the thermodynamic properties of such waters.
Hope this helps,
-Dan
>
> Thanks and Regards,
>
> -Tian
>
>
> >Date: Mon, 20 Dec 2021 09:56:28 -0500
> >From: Daniel Roe <daniel.r.roe.gmail.com>
> >To: AMBER Mailing List <amber.ambermd.org>
> >Subject: Re: [AMBER] Hydrogen Bonding Analysis
> >Message-ID:
> <CAAC0qOaSUcPJE4-SbFTNZ58q0f=Bfgm4xAET1GaQ5VdnFwC8wg.mail.gmail.com>
> >Content-Type: text/plain; charset="UTF-8"
>
> >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
>
>
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Received on Wed Jan 05 2022 - 06:30:02 PST
