Dear Vaibhav
In my opinion you can not use a simple 0.9 value for the Mg charge
without considering the charge distribution
on the residues interacting with the ion.
There are different recipes to simulate ions in bio-inorganic systems.
Maybe you can check:
Dal Peraro et al. Modeling the charge distribution at metal sites in
proteins for molecular dynamics simulations (2007)
Journal of Structural Biology.
or also this
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1859854/
Jacopo
2011/4/15 Vaibhav Jain <xtreme.vaibhav.gmail.com>:
> Dear AMBER users,
>
> I have protein in which Magnesium ion is forming octahedral coordination
> geometry with the atoms of active site viz. 3 point interactions with the
> ligand oxygens, 2 interactions with conserved water molecules and 1
> interaction with side chain oxygen of Asn amino acid. My main concern is
> about the effective charge on the Magnesium ion. I read literature where
> they have used charge on Mg as 0.9 instead of +2, due to distribution of
> electrons between the interacting atoms.
>
> While preparing the input files inpcrd and prmtop for protein in AMBER, I
> found that total effective charge on protein is 5.9 (including charge 0.9 of
> Mg). So accordingly I added 5 Cl- ions to it. But, keep the total charge as
> +0.9 (Mg). Is it a correct way to perform dynamics or otherwise I have to
> add 1 more Cl- ion to make the effective charge as -0.1.
>
> Please help me in this regard.
>
> Thanks a lot.
>
>
> --
> *Warm Regards *
>
> Vaibhav Jain
> Ph.D. Scholar
> Centre For Pharmacoinformatics
> NIPER, Mohali (Punjab)
> MOb no. +919988412195
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Received on Fri Apr 15 2011 - 08:30:02 PDT
