[gmx-users] Exotic metal species
lpeng at ucsd.edu
Thu Aug 13 22:53:15 CEST 2009
Thanks for your comments. There is a group that has developed force field
parameters for the Indium(III)-DTPA using Amber:
http://www.ncbi.nlm.nih.gov/pubmed/11559086 . Since the authors were able
to successfully determine force field parameters for Amber, a molecular
dynamics package, can I safely assume that charge transfer is not an issue
for running simulations on In(III)-DTPA using another MD-based package like
2009/8/12 David van der Spoel <spoel at xray.bmc.uu.se>
> 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).
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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
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