AMBER: DOTA-Lanthanide complexes in Amber

From: <>
Date: Tue, 15 Aug 2006 13:48:23 -0400

Dear Amber Community,

I have been working on incorporating Gadolinium bound to its DOTA ligand
into Amber 7. The big problem that needs to be worked out with this is
the limit on the number of bonds a given atom can form using Amber 7.
Using several papers published on incoporating Gadolinium into other
force fields as guidance I think I have a solution, but I wanted to check
if anybody knows of a better approach.
Due to the limitation in the number of bonds, I created bonds that would
normally not be formed to force the Gd-DOTA complex into the “correct”
shape. I realize this is uncommon and could clearly not be used to study
the structure of the Gd-DOTA complex itself, but the purpose for our work
is only to study the effects of the complex on a macromolecule that it is
attached to.

Is anybody aware of a better workaround to this issue?

Is there a way in Amber that I can check the MD results of this against
crystal structure data?

Best Regards,


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Received on Wed Aug 16 2006 - 06:07:22 PDT
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