Hi Eliac,
> I am trying to simulate some aromatic molecules in gas phase and in
implicit
> 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
without
> 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
semi-empirical.
Good luck,
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Jan 11 2011 - 10:00:04 PST
