From: Jan Saam (saam_at_charite.de)
Date: Mon Aug 28 2006 - 05:46:22 CDT
yes, Mackerell's procedure can become rather complicated and there is no
simple shortcut. Mullikan charges are about the worst approximation you
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 Germany +49 30 450-528-446 saam_at_charite.de
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