[gmx-users] Exotic metal species

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 13 08:08:15 CEST 2009

Lili Peng wrote:
> Der all,
> I'd like to know if any has had experience in using GROMACS for modeling 
> exotic metal species like Gadolinium(III) and Indium(III)?  My system is 
> actually an Indium(III) ion coupled to  DTPA 
> (diethylenetriaminepentaacetate), an octadentate ligand forms bonds with 
> metals through three atoms of nitrogen and five atoms of oxygen.  I've 
> consulted the Gromacs wiki 
> (http://www.gromacs.org/WIKI-import/Exotic_Species) and it suggests that 
> I consult someone with expertise in this area.  Has anyone had any 
> (successful?) experience in this effort?
It depends on what the ion does, if it only has a structural role, and 
is not exposed to solvent, you can model it as any 3+ charge site, and 
use covalent bonds or distance restraint to keep it in place. However, 
if the ligands are supposed to move away from the ion it becomes 
complicated. In any such interaction charge transfer is significant, but 
difficult to quantify, and very difficult to model with clasical models 
(and with QM models for such a big guy).

> Thanks,
> Lili
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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