Re: add calcium chloride

From: Peter Freddolino (
Date: Mon Apr 07 2008 - 08:09:58 CDT

Hi Christine,
fastest way to do this is probably to add sodium chloride with
autoionize, adding a user defined number of cations and anions to get
the appropriate ratio, and then change all the sodium to calcium (with,
eg, sed or a text editor) in the output pdb and rebuild your psf. If you
don't mind a little more hand editing, you can just change the sodium to
calcium right in the autoionize output psf (be sure to get the mass,
charge, name, etc) as well as the pdb. Allowing autoionize to add
arbitrary ions is on the wishlist but no one has had time to do this yet...

Christine Horejs DI wrote:
> Dear all,
> I have a protein dissolved in water and now I would like to add
> calcium chloride to the water molecules (10mM)! How can I do this? Is
> it possible by using the autoionize package of VMD?
> Thank you for your help!
> Greetings from Vienna, Austria,
> Christine Horejs

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