From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Apr 16 2008 - 10:12:24 CDT
I put together a vmd script to pick waters from bulk in a system and
randomly convert them to Na and Cl.
see my DashOfSalt script at
This can be easily modified to change number and type of ions.
It runs fast but that's because it picks waters at random rather than
doing any electrostatic calcs.
On Wed, 2008-04-16 at 14:30 +0200, Christine Horejs DI wrote:
> Thank you for the tip! I tried to use autoionize and it works, but not
> exactly as I want to!
> I would like to add 10mM CaCl, that means I need twice as much Ca than Cl! I
> used the following command:
> autoionize -psf silc.psf -pdb silc.pdb -nna 50 -cl 100
> and then I wanted to change the ions directly in the pdb and psf files!
> but this doesn't work!
> Do you have any idea? Would be great help!
> ----- Original Message -----
> From: "Peter Freddolino" <petefred_at_ks.uiuc.edu>
> To: "Christine Horejs DI" <horejs_at_gmx.net>
> Cc: <namd-l_at_ks.uiuc.edu>
> Sent: Monday, April 07, 2008 3:09 PM
> Subject: Re: namd-l: add calcium chloride
> > 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...
> > Best,
> > Peter
> > 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
-- *********************** * Thomas C. Bishop * *Office: 504-862-3370 * *CCS: 504-862-8391 * *Fax: 504-862-8392 * ***********************
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