Re: [AMBER] Protein nanoparticle interaction

From: Ben Roberts <>
Date: Wed, 25 Apr 2012 14:42:58 +1200

Hi Navin,

On 24/04/2012, at 9:56 PM, Navin Jain wrote:

> I would like to investigate the interactions of silver nanoparticles
> with a protein moiety. Can anybody help me to prepare the parameter
> file of a silver nanoparticle to carry out molecular dynamics???

As you've probably gathered from the silence on this thread, the answer to your question is almost certainly no.

AmberTools includes packages to help prepare parameters for small organic molecules (Antechamber) or transition-metal complexes (MTK++), and there is also the third-party tool R.E.D. that computes atomic charges and may serve other purposes. But I'm not aware that any of these tools will help you directly with metal clusters.

In general, we can't offer help to compute or validate parameters. The parameter generation process is long and complex, and outside the scope of the volunteers and fellow users who populate this list. The best way to get help is to do background reading on what you want to do, look at the Amber manuals and tutorials, and then come back to us with specific questions.

Hope that helps,


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Received on Tue Apr 24 2012 - 20:00:04 PDT
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