You can do that using the option 'ion'. For example, for a concentration of 150mM of sodium, you'll need to have something like this in your input file:

ion 1 0.150 2

The first value is the charge (+1), whereas the other two values indicate the ion concentration (in moles) and radius, respectively.


On Tue, Sep 1, 2009 at 4:33 PM, Raluca Mihaela ANDREI <> wrote:
Michel, thank you for your answer, but I definitely didn't say clearly which my problem is. Sorry! I would like to know how to set the ion concentration and ion radius if I want to use APBS from the command line, without using VMD, using as input file an .in file obtained with pdb2pqr.

On Tue, 1 Sep 2009 16:25:54 +0200
 "L. Michel Espinoza-Fonseca" <> wrote:
Hi Raluca,

As this question is VMD-related, you'll have higher chances of getting the
answer you need if you refer your question to the VMD mailing list. Keep
this suggestion in mind for the future.

You can easily change these parameters if you go select your individual PB
calculation in the APBS tool window, then click on 'Edit'. You should find
another button called 'Edit' just right in front of the 'Mobile ions'
option. This will allow you to change both values of ion concentration and


On Tue, Sep 1, 2009 at 3:02 PM, Raluca Mihaela ANDREI <>wrote:

when I use APBS as a plug-in for VMD, I noticed that Mobile
ion concentration and mobile ion species radius is already
set. How can I set these 2 parameters if I use APBS from the
windows command line. I use APBS 1.1.0.
Thank you,

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