AMBER Archive (2006)

Subject: Re: AMBER: PKDIV lone pair dihedrals

From: David A. Case (
Date: Mon Oct 23 2006 - 15:26:58 CDT

On Mon, Oct 23, 2006, Lorenzo Gontrani wrote:

> Dear amber users, I am building the topology of a molecule with several
> explicit lone pairs (around C=O fragments). I was wondering if anyone knows
> why all the PKDIV values of lone-pair torsions are set to zero (parm99).
> Maybe it is a stupid question..lone pairs are "kept" by BOND and ANGLE
> parameters, they are enough..

Lone pairs are kept "in place" by rigid body constraints, and always move
synchonously with the heavy atoms they are attached to. The bond and angle
force constants involving them are ignored, but the equilibrium bond lengths
and angles are used to set the corresponding distances and angles. I believe
that all of the torsion parameters involving lone pairs are ignored.
(Tom Darden can chime in here if this is not correct....)


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