Hi Zhou,
I am copying this to the amber list which is where such questions are best
posted. See
http://ambermd.org/ 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:
list
And it will show you all the units it knows about from which you can
identify the ions.
All the best
Ross
From: zgong.hust [mailto:zgong.hust.gmail.com]
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
2009-05-20
_____
Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
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Received on Wed May 20 2009 - 17:40:19 PDT
