From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Aug 28 2006 - 10:10:05 CDT
About the partial charges, I completely agree with Jan. There are
interesting comparisons of different models used to get partial
charges vs level of theory and basis. The results obtained so far
showed that the Mulliken analysis is not consistent at all when you
pick two different basis at the same level of theory. You can even get
contradictory results... So, as Jan pointed out, the worst model you
can use is the Mulliken one! I would tell you something: NEVER, NEVER
use Mulliken for parametrization and/or analysis purposes. This might
be redundant for many people, but I think it is worth to mention :)
2006/8/28, Jan Saam <saam_at_charite.de>:
> Dear Luca,
> yes, Mackerell's procedure can become rather complicated and there is no
> simple shortcut. Mullikan charges are about the worst approximation you
> can use.
> If your molecule is complex you must split it into smaller model
> compounds and determin the charges for the smaller compounds separately.
> Also you can try to assign some of the charges by analogy: i.e. if a
> part of your molecule matches one of the GROUPs in an existing Charmm
> molecule, e.g. a carboxylate group, you can use these charges.
> VMD's plugin Paratool will eventually support semiautomatic
> determination of charmm charges. In fact the code is there already but
> it's not complete yet. Watch out for updates of the plugins, I hope to
> find the time to finish this part of paratool in a couple of weeks.
> Luca Bellucci wrote:
> > Hi ALL
> > In order to obtain partial atomic charge in CHARMM potential. Sometime is
> > "impossible" to perform the Dr. MacKerell's procedure in reasonable times.
> > Complex molecules or a lot of molecule do not allow this type of approach.
> > Is there a simple method or article that explain how to do this?
> > Can I use only Mulliken charge of the molecule without water (first
> > approximation charge) ?
> > Thank you very much for any help and information.
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> +49 30 450-528-446
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:30 CST