Re: AMBER: Shake&Lone Pairs

From: David A. Case <>
Date: Wed, 25 Oct 2006 11:21:02 -0700

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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 29 2006 - 06:07:08 PST
Custom Search