Re: Ionize script

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 08 2010 - 11:52:45 CDT

no need for this kind of complication. i didn't realize what the
real issue was. this step is _even_ easier to do with a few commands.

set sel [atomselect top all]
$sel set beta [$sel get charge]
$sel writepdb filewithchargeinbeta.pdb

done.

cheers,
    axel.

On Thu, Apr 8, 2010 at 11:55 AM, <ehenriques_at_qui.uc.pt> wrote:
> Quoting Tommy Kahn <tk7434_at_gmail.com>:
>
>> I am attempting to use the Ionize software as described here:
>> http://www.ks.uiuc.edu/Development/MDTools/ionize/
>>
>> It requires an input pdb with the charge on each atom in the value of
>> "beta". Is there a way to enter these values in an efficient manner, such
>> as
>> with VMD's tk console?
>>
>
>
> Provided you already have a .psf associated with your .pdb, if you upload
> both to VMD and then Save Coordinates in BIOGRF format (.bgf), you'll end up
> with a file with a column with all the charges (that you can then copy/paste
> in one go to your pdb).
>
>
> Elsa
> ------------------------------------------------------------------
> Elsa S. Henriques                     e-mail: ehenriques_at_qui.uc.pt
> Investigadora Auxiliar
>
> Biologia Estrutural e Computacional (@CNC)
> e Grupo de Química Estrutural (@CCC)
> Cv15 - RMB Lab
> Departamento de Química - Universidade de Coimbra
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>
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>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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