VMD-L Mailing List

From: Qiang Fu (qiangfu.music_at_gmail.com)
Date: Fri Feb 25 2011 - 09:48:45 CST

Dear VMD Users,

I want to draw a figure to show a molecule adsorbed on a metal surface.
However, there is no bond connection between metal atoms even I used the
CPK mode for display, which makes the current version of the figure
unacceptable.

>From the discussions on the VMD Mailing list, I know that with the command
"topo addbonds <ID1> <ID2>, one can add a bond between the two atoms <ID1>
and <ID2>. However, there are as many as 64 atoms in our surface system,
which makes it too complicated to achieve in the same way. I know the Tk
Console script might be used to do so, but I have very very little knowledge
about it.

Could you please give me some help? I am very grateful if you could tell me
some convenient way to add bonds among so many atoms within the metal
surface. Thank you very much!

Best Regards!
Sincerely,
Qiang Fu 

-- 
Dr. Qiang Fu
Major in computational chemistry
E-mail: qiangfu.music_at_gmail.com
Profile URL: http://www.researcherid.com/rid/A-2557-2011