AMBER Archive (2006)

Subject: Re: AMBER: Shake&Lone Pairs

From: David A. Case (
Date: Wed Oct 25 2006 - 13:21:02 CDT

On Wed, Oct 25, 2006, Lorenzo Gontrani wrote:

> Dear AMBER users, does anybody have experience about using SHAKE when extra
> points are defined on several atoms (C=O lone pairs)?
> After equilibrating the water molecules box around my lone-pair containing
> solute, I always get SHAKE errors whenever I release the solute constraints
> (or I remove water BELLY). I checked with ptraj/checkoverlap and all the
> short contacts are due to LP-heavy atom interactions.

Lone-pairs are very tricky, and it is not uncommon to see shake failures
even with "established" parameter sets such as ff02EP. I definitely think
that more parameterization work is needed in this area if this is to be a
useful way to do things; (and the testing needs to involve fairly long
simulations, since these problems don't always show up just with

As usual, others are welcome to chime in here; my understanding is that the
UCD group has also seen similar failures.


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