Re: add calcium chloride

From: Christine Horejs DI (
Date: Wed Apr 16 2008 - 08:22:28 CDT

It already worked!


----- Original Message -----
From: "Christine Horejs DI" <>
To: "Peter Freddolino" <>
Cc: <>
Sent: Wednesday, April 16, 2008 2:30 PM
Subject: Re: namd-l: add calcium chloride

> 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!
> Greetings,
> Christine
> ----- Original Message -----
> From: "Peter Freddolino" <>
> To: "Christine Horejs DI" <>
> Cc: <>
> 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

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