Re: [AMBER] MD simulation by amber

From: Hai Nguyen <>
Date: Tue, 15 Nov 2016 21:40:12 -0500

I do not have answer for you and seems that you have not got any reply. So
I bump this email here so other can see it.
Please make your email title more descriptive than just "MD simulation by
[Due to large amount of emails everyone get everyday, it's very easy to
skip one if the title is not "right"]

cheers and good luck.

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.
> Regards,
> Yeganeh
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Received on Tue Nov 15 2016 - 19:00:02 PST
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