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CHARMM parameters for Mn2+
#37861 05/01/20 05:55 PM
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Dear all,
I want to run a MD simulation of Mn2+ bound protein but I could not find CHARMM parameters for Mn2+. I came to know that transition metals are highly problematic, as they are typically present as a complex with a different specific geometry depending on the oxidation state and available ligands.
In my system, Mn2+ in complex with Glu, Asp, His, and 2 water molecules. So how can I get Mn2+ CHARMM parameters for my system?

Many thanks for your kind attention.
Abhishek

Re: CHARMM parameters for Mn2+
Abhishek.2015 #37862 05/03/20 04:44 PM
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As you may have noticed, the answer to this question has not changed for the past 16 years or more.

How you approach this depends on the importance of the Mn++ binding site in the study being considered. If you only need it as a structural element, unrelated to the rest of the study, stabilizing the preferred binding geometry with restraints may be the best approach. For that, you should undertake a review of relevant crystal structures, esp. those with good resolution for the complexation site, to determine a reasonable geometry.


Rick Venable
computational chemist


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