AMBER Archive (2009)

Subject: [AMBER] RE: add magnesium

From: Ross Walker (
Date: Wed May 20 2009 - 16:30:09 CDT

Hi Zhou,


I am copying this to the amber list which is where such questions are best
posted. See for details.


Adding Mg2+ ions should be as simple as adding Na+, Cl- etc. You just use
the addions command in the same way it is covered in Tutorial B1 on the
amber website.


addions unit MG2 x


Where x is the number of Mg2+ ions you want to add.


For a list of ions currently loaded in leap you can type:




And it will show you all the units it knows about from which you can
identify the ions.


All the best



From: zgong.hust []
Sent: Wednesday, May 20, 2009 7:34 AM
To: Ross Walker
Subject: add magnesium


Dear sir:

          I would like to add magnesium to the RNA molecule before perform
the MD simulations. How can I add the magnesium ions using tleap?

What kinds of ions could I add by using the tleap?



Thank you very much for your help



Zhou Gong

School of Physics

Huazhong University of Science and Technology


Hubei Province


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