> 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
website
http://amber.scripps.edu/tutorial/polyA-polyT/index.html
All the best
Ross
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Feb 24 2004 - 18:53:01 PST
