Re: [AMBER] Tleap parametrisation of NA+ bound proteins

From: David A Case <>
Date: Tue, 1 Aug 2017 13:23:42 -0400

On Tue, Aug 01, 2017, James Starlight wrote:
> I need to include in a model a metal cofactor (Na+ ion) embedded
> within an allosteric pocket on the protein. Here I would like to
> parametrize the ion as non-bonded model.
> Assuming that I know the position of the NA from a given pdb, which
> parametres should I use for tleap for the parametrisation of the
> complex and how I should name NA within the input pdb?

NA ions are standard in Amber, and get loaded along with the corresponding
water models in the leaprc.water.* files. You should follow the PDB standard,
and name both the atom and the residue as NA in your input pdb file.


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Received on Tue Aug 01 2017 - 10:30:02 PDT
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