Re: [AMBER] MD simulation by amber

From: David A Case <>
Date: Wed, 16 Nov 2016 09:00:38 -0500

On Tue, Oct 4, 2016 at 12:52 PM, Atila Petrosian <>

> Dear amber users,
> Hi, I want to do molecular dynamic simulation with amber. The condition of
> my protein-ligand system are following as: my protein has Zn+2 ion in the
> active site which three histidine coordinate with it by covalent bond. Also
> my ligands are sulfonamide and have -1 charge on nitrogen atom which are
> oriented from nitrogen atom toward zinc ion in the active site of the
> protein.
> I wonder if you recommend me a suitable amber tutorial for such kind of
> system I explain.

Have you looked at tutorial A20, "Metal Ion Modeling Tutorial"?


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Received on Wed Nov 16 2016 - 06:30:03 PST
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