Re: add calcium chloride

From: Christine Horejs DI (horejs_at_gmx.net)
Date: Wed Apr 16 2008 - 07:30:41 CDT

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" <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

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