Hi Andrew,
> I actually wonder that if Zn is bound but not ion, probably it can
> influence geometry of the whole protein if I parametrize it as an ion.
> Probably I should fix Zn residue and amino acid residues which are
> bound to it. I think it is reasonable.
This is very much a try it and see situation. I would start by just doing a
2+ ion and see what happens. Note fixing the surrounding residues may not be
as easy as it appears at first since really you need to fix them with
respect to each other and the zinc ion rather than to a fixed starting
structure. You could always add bond, angle and dihedral terms that are
sufficiently stiff to accomplish the same type of restraints.
Good luck,
Ross
/\
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
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http://www.wmd-lab.org/ |
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Received on Thu Jan 14 2010 - 12:00:02 PST
