AMBER Archive (2004)

Subject: Re: Fwd: Re: AMBER: Pang-model of Zn2+

From: David A. Case (
Date: Fri Mar 26 2004 - 16:18:35 CST

On Fri, Mar 26, 2004, Oliver Hucke wrote:
> thanks a lot for your comments on my questions regarding the cationic
> dummy atom approach to modeling Zn+2!
> The first thing I was looking at after encountering the fusion problem
> were indeed the van der Waals radii of the zinc and the hydroxyl-oxygen.

I have not used the "dummy atom Zn+2 model", but this sounds very much like
what happens with common water models, like TIP3P. With a "flexible" water,
the L-J terms on the oxygen are not necessarily enough to keep the proton
from moving away from its own oxygen, and "fusing" into the oxygen on another
water molecule. Depending on how the simulation proceeds, one may be "lucky"
and not have this happen, but there is nothing in the force field that
prevents this.

Of course, TIP3P is really defined as a "rigid" system, and such behavior will
not occur when the O-H distance is fixed (shaken), rather than contrained by a
bond term. My guess is that the same thing will be required for the Zn-dummy
atom model.

As I said, this comment is based on general knowledge, not on any specific
experience with this model for Zn coordination.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to