Re: [AMBER] Lifetime structural waters CPPTRAJ error

From: Daniel Roe <>
Date: Thu, 24 Jan 2019 10:45:05 -0500

This information is in the file written by the 'out' keyword as
described in the manual (section 30.10.35 hbond):

[out <filename>] Write # of solute-solute hydrogen bonds (aspect [UU])
vs time to
this file. If searching for solute-solvent hydrogen bonds, write # of
solute-solvent hydrogen bonds (aspect [UV]) and # of bridging solvent
molecules (aspect [Bridge]), as well as the residue # of the bridging
solvent and the solute residues being bridged with format ’<solvent
resnum>(<solute res1>+<solute res2>+...+),...’ (aspect [ID]).

Hope this helps,


On Thu, Jan 24, 2019 at 7:24 AM Pedro Miguel Reis Figueiredo
<> wrote:
> Hi,
> I am running some analysis on lifetime of structural waters. I
> need to know which waters (from solvent - TIP3PBOX) are performing
> bridge bonds with residues responsible to keep the protein structure.
> I have followed the tutorial "Hydrogen bond analysis with CPPTRAJ" by
> Daniel Roe but cannot find the ID of waters that are performing such
> bonds in the output files..
> Is there any command to get the waters ID?
> Thank you in advance.
> _______________________________________________
> AMBER mailing list

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Received on Thu Jan 24 2019 - 08:00:05 PST
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