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 <sp...@xray.bmc.uu.se
<mailto:sp...@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 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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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
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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