Hi Nicee,
> I am having a protein which is negatively charged. the protein has 9
> Ca+binding
> motif and I want to check whether it is of Ca+2 binding or not. So i
> want to
> simulate it in presence of Ca++ ions. Should I neutralize the protein
> before
> minimization or not.
This depends. What do the experimental conditions look like? This would give you an idea of how best to proceed. Probably it is calcium binding in some kind of salt solution such as calcium chloride. In which case I would probably add the Calcium close to the binding site and then sufficient Cl- ions to neutralize the protein + the Ca2+ ions. Although you might want to add more ions if the experiment was done in some high salt concentration.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Sun Jan 24 2010 - 22:30:03 PST
