[AMBER] Extra Bonds For Water

From: Kyle Greenway <kgreenwa.sfu.ca>
Date: Tue, 13 Mar 2012 15:37:33 -0700 (PDT)

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?


Kyle Greenway
AMBER mailing list
Received on Tue Mar 13 2012 - 16:00:02 PDT
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