From: Ross Walker <>
Date: Tue, 11 Jan 2011 09:58:17 -0800

Hi Eliac,

> I am trying to simulate some aromatic molecules in gas phase and in
> solvent using amber 10 at QMMM level.
> One of the studied molecules is simple chlorobenzne using PM3 level to
> describe the molecule. In the gas phase, the minimization is finished
> any problem, but in implicit solvent using IGB=2, the molecule changes its
> structure to give a half-chair model.
> How can I solve this problem?
> Is that related to the PM3 parameters or to amber code?

Unfortunately this is an issue with the parameters. And also the fact that
while GB works in theory with semi-empirical QM it has not been necessarily
been optimized for this. I would suggest trying some alternative GB models
as well as some of the alternative semi-empirical models. It is also
possible that one might need to consider optimizing the GB radii for

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Jan 11 2011 - 10:00:04 PST
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