Re: [AMBER] Extra Bonds For Water

From: Adrian Roitberg <>
Date: Tue, 13 Mar 2012 18:44:59 -0400

The definition of TIP3P is for a rigid water molecule. This can be
achieved by constraining bond lengths and the angle, OR by having 3
bonds and constraining them.

That last one is what is implemented in amber (and many other force fields).

So, nothing to worry about, but it is a good question.


On 3/13/12 6:37 PM, Kyle Greenway wrote:
> Hello All,
> (Apologies if this is similar to a previous email I sent but that seems to have been caught up in moderation).
> I've noticed that water molecules added in leap, or imported from a pdb into leap, are consistently created with bonds between the hydrogens. You can see this visually in xLeap, or by using the desc command, for example:
> desc mol.867.3
> Normal Perturbed
> Name: H2 H2
> Type: HW HW
> Charge: 0.4170 0.000
> Polarization: 0.0000 0.000
> Element: H (not affected by pert)
> Atom flags: (decimal 131072 hex 0x20000)
> posfxd n posblt n posdrwn n selected n
> pert n notdisp n touched n posknwn Y
> internal n needsmin n needsbuild n
> Atom position: -12.913000, -21.637000, 6.567000
> Atom velocity: 0.000000, 0.000000, 0.000000
> Bonded to .R<WAT 867>.A<H1 2> by a single bond.
> Bonded to .R<WAT 867>.A<O 1> by a single bond.
> Unsurprisingly these extra bonds are specified in the relevant ion parameter files. I've only found this for the TIP3P model but it might be more general. My question is then twofold: why is this happening, and is it anything to worry about?
> Regards,
> Kyle Greenway
> _______________________________________________
> AMBER mailing list

                            Dr. Adrian E. Roitberg
                Quantum Theory Project, Department of Chemistry
                            University of Florida
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Received on Tue Mar 13 2012 - 16:00:03 PDT
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