[Chimera-users] Drug-Metal Complexation Modeling

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 23 09:23:31 PDT 2011

Hello Mickey,
Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal.  It is intended for use with existing coordinates, such as from crystallography or output by other computational methods.  Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place.


You can build structures with Chimera, but optimization is rather limited to only a few metals, and  those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality).  It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs.


I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 22, 2011, at 11:11 PM, Mickey Branham wrote:

> Dr. Meng
> Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2.
> Cheers
> Mickey
>  Michael Lee Branham, PhD.
> University of KwaZulu-Natal
> School of Pharmacy and Pharmacology 
> Durban, South Africa
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