From: David Case <>
Date: Thu, 24 Feb 2011 22:20:18 -0500

On Feb 24, 2011, at 6:18 PM, Jorgen Simonsen <> wrote:

> and thanks for the response so I am adding a copper ion to a histidine
> and as it might have other interactions with nearby residues I have
> changed the type of NE2 to UA - yhe problem is that when I have
> generate the inpcrd and prmtop and look at the pdb file(ambpdb from
> ambertools) the imidazole ring has lost its planarity - having a boat
> shape.

Did you do a minimization or anything? When you "generate the inpcrd" in tleap, it is just using whatever coordinates you give it.

You might also check to see if you are missing any improper terms that would ordinarily keep planarity about the NE2 atom.


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Received on Thu Feb 24 2011 - 19:30:05 PST
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