Hi David,<br><br>Thanks for your comments. There is a group that has
developed force field parameters for the Indium(III)-DTPA using Amber: <a href="http://www.ncbi.nlm.nih.gov/pubmed/11559086">http://www.ncbi.nlm.nih.gov/pubmed/11559086</a> . 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?<br>
<br>Thanks,<br>Lili<br><br><div class="gmail_quote">2009/8/12 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Lili Peng wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Der all,<br>
<br>
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 (<a href="http://www.gromacs.org/WIKI-import/Exotic_Species" target="_blank">http://www.gromacs.org/WIKI-import/Exotic_Species</a>) and it suggests that I consult someone with expertise in this area. Has anyone had any (successful?) experience in this effort?<br>
<br>
</blockquote></div>
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).<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks,<br>
Lili<br>
<br>
<br>
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David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
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