From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Apr 24 2009 - 11:37:09 CDT
On Fri, 2009-04-24 at 20:02 +0400, DimitryASuplatov wrote:
> Hello,
>
> Im trying to simulate a copper binding protein. I did not find copper
> ion in charmm files.
>
> 1/ I`ve found those parametern on one of the CHARMM forums
> (http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=16041&Main=15961)
> They were claimed to be from Deng et al Biophysical Journal 2006. I
> did not find them in this paper though.
>
> What do you suggest? Does anyone used any other parameters for copper?
> ! Emin(kcal/mol) ! Rmin(A)
> MCU 0.00 -0.060 1.380
>
> MASS 96 MCU 63.546 Cu ! Copper
>
>
> 2/ Why copper is absent from CHARMM topology? It sound like some kind
> of problem with universal one-far-all parametrization of this ion.
dimitry,
this is a general problem. most metal ions except for light monovalent
one cannot be represented by a pair-wise additive potential. for higher
oxidized cations you usually have some "back-donation" of the charge,
so the ion has, say, +1.6 effective charge and 4 coordinated water or
other atoms have correspondingly adjusted partial charges. this is why
people do QM/MM on metal atom containing enzymes, and even there you
can quickly run into problems with the high multi-reference character
of the electronic structure. transition metals are especially nasty.
some people prefer to be ignorant of this and say they do the best
they can. former colleagues of mine have use QM/MM calculations with
force matching to reparameterize such active enzyme centers,
but then resulting parameters are specific for this configuration.
hope that helps.
cheers,
axel.
>
> Thanks.
> SDA
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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