[gmx-users] Exotic metal species

[David van der Spoel]

Lili Peng wrote:
> Hi David,
> 
> 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 Gromacs?

No you can not assume that. I have not read the paper an am not familiar 
with the system, but you need to be cautious when using this kind of 
model. If you use the Amber force field with these parameters you can of 
course cite this paper and probably get away with it, but be aware of 
the intrinsic problems with these system.
> 
> Thanks,
> Lili
> 
> 2009/8/12 David van der Spoel <spoel at xray.bmc.uu.se 
> <mailto: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).
> 
>         Thanks,
>         Lili
> 
> 
>         ------------------------------------------------------------------------
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> 
> 
>     -- 
>     David.
>     ________________________________________________________________________
>     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 <mailto:spoel at xray.bmc.uu.se>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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-- 
David.
________________________________________________________________________
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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