AMBER Archive (2009)

Subject: [AMBER] RE: add magnesium

From: Ross Walker (ross_at_rosswalker.co.uk)
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 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_at_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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