From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Wed Nov 19 2008 - 10:07:33 CST

This is what I understood Bo Liu... I did some calculations yesterday, and I found out the conc of normal saline is 0.15 - I think I did it right, do you think that if I want to simulate the human cell/fluids I need to setup the concentration according to that of the normal saline...I am not a Biologist but I am trying to figure out what would be the best concentration to set in order to mimic the biological conditions.

JC, I would try your 0.0001 because for now I need to neutralize only 4 positive charges on a small peptide. I would also try the NCl and see.

Many thanks
Rabab

--- On Wed, 11/19/08, bo liu <liubo.njuer_at_gmail.com> wrote:
From: bo liu <liubo.njuer_at_gmail.com>
Subject: Re: vmd-l: Autoionize plugin
To: "JC Gumbart" <gumbart_at_ks.uiuc.edu>
Cc: rtoubar_at_yahoo.com, vmd-l_at_ks.uiuc.edu
Date: Wednesday, November 19, 2008, 9:42 AM

Hi Gumbart,
 
you mean that if i want to keep the ion concentration of my system at 0.15M, what i have to do is to set it as 0.30M with autonionize?
 
Bo

2008/11/19 JC Gumbart <gumbart_at_ks.uiuc.edu>

The value given is just an example, you should take it with a grain of salt.  (hahaha)   There is not a default value; you either must give a concentration or a fixed number of ions.

 
The autoionize gui plugin has an option to only neutralize the system; alternatively, you could just specify –is .0001 to make it only place enough ions to neutralize the system and no more (assuming this is what you want to do).  Physiological concentrations are definitely higher than 50 mM, more like 150 mM, I think, although the relevant ion species and concentrations vary so consider the native environment of your system carefully.  Keep in mind though that the concentration in the autoionize plugin is effectively twice that in experiments (i.e. 150mM KCl in experiment -> 300mM total ion concentration (K+ and Cl-) in autoionize).

 
 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Rabab Toubar

Sent: Tuesday, November 18, 2008 7:40 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Autoionize plugin

 

Hi all,

 

1- I was wondering what is the importanced of the ionic concentration in the mentioned script at this webpage: http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/

 

autoionize -psf file.psf -pdb file.pdb -is 0.05

 

Is it to resemble the physiological pH? What if I didn't include it in the script, is there a default value for it?

 

2- Which would be more accurate: calculating the net charge on the peptide and specifying the number of opposiite charge to neutralize it - provided it is reasonably small, or using the autoionize

 

Thanks

Rabab
 

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-Bo Liu
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