AMBER Archive (2004)

Subject: RE: AMBER: add Na+

From: Ross Walker (
Date: Tue Feb 24 2004 - 12:42:28 CST

> I want to add 3 Na+ to my molecule. I found that there is Na
> ion in ion94.lib.
> But it seems that it is invisible. I am curious why it is
> like this. How can I
> make it visible when I add 3 Na+ to my molecule? Thanks in advance.

Open your molecule in xleap:

model = loadpdb myfile.pdb

and then run the command:

addions model Na+ 3

This will create a 1 angstrom resolution charge grid around your molecule
and add 3 Na+ ions at the three points of highest negative potential.

For more info refer to the xleap manual or the DNA tutorial on the amber

All the best

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