Re: [AMBER] Individual bridging water lifetimes by closest?

From: Daniel Roe <>
Date: Tue, 3 Jul 2018 08:38:45 -0400

On Mon, Jul 2, 2018 at 4:18 PM, Kenneth Huang <> wrote:
> Thanks for the pointers- it does sort of works for my system, but it does seem to get thrown off every once in a while in picking waters by the geometric center. I'll keep fiddling with it to see if I can't get it to work properly. Is there a way for hbond to print out the atoms that are getting bridged along with the molecule?

Yes, use the 'bridgebyatom' keyword. Another thing to keep in mind is
that by default 'hbond' uses an angle criterion in addition to
distance, while the script I gave you is distance only. Maybe that
accounts for some of the discrepancy?

> Also, am I correct in assuming that using the center keyword with closest makes it use the geometric center vs the center of mass that distance uses?

Not exactly. When 'center' is specified, 'closest' will determine the
closest solvent molecules to the geometric center of the atoms in
<mask>. When not specified (i.e. the default behavior) 'closest' will
determine the closest solvent molecules to *any* atom in <mask>. The
latter behavior is useful for when you want something like a solvation
shell around your solute.


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Received on Tue Jul 03 2018 - 06:00:02 PDT
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