AMBER Archive (2006)

Subject: Re: AMBER: PKDIV lone pair dihedrals

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Mon Oct 23 2006 - 16:05:37 CDT

I believe Dave is right here
Tom D

On Mon, 23 Oct 2006, David A. Case wrote:

> 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....)
>
> ...dac
>
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