Re: third time..can someone help!!

From: Edelmiro Moman (moman_at_titus.u-strasbg.fr)
Date: Wed Jul 12 2006 - 02:40:03 CDT

Most commercial packages include routines for adding counterions to a
biomolecule. But there are also a few free packages such as VEGA:

VEGA OpenGL (http://www.ddl.unimi.it)

You can also try a number of VMD plug-ins, other than Autoionize:

http://www.chem.duke.edu/~ilya/software/Meadionize/docs/meadionize.html

or

http://www.ks.uiuc.edu/Development/MDTools/wat2ions/

or

http://www.ks.uiuc.edu/Development/MDTools/sodium/

As you can see, the last two ones are in the NAMD website. If you do
some googling you are likely to find more stuff.

hl332_at_drexel.edu wrote:
> Hi all,
> I want to add ions in my system other than sodium and pottasium as given in autoionize plugin manual. It (explicitly TCL SCRIPT) also says how to change different ions but i dont know what to do if i want to add HCO3-(bicarbonate ions) and moreover at a later stage if i want to add divalent ions. please help!!!
> Regards and thanks in advance...
> Harish...
>
> -------------------------------------------------
> Harish Vashisth
> Graduate Student(Ph.D)
> CAT-361,Department of Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>
>

-- 
Edelmiro Moman
Institut de génétique et de biologie moléculaire et cellulaire
Laboratoire de biologie et de génomique structurales
1, rue Laurent Fries
F-67404 Illkirch Cedex
FRANCE
Tél. : +33 (0)3 88 65 3309
Fax : +33 (0)3 88 65 32 76
moman igbmc u-strasbg fr

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