Re: Ionize script

Date: Thu Apr 08 2010 - 10:55:44 CDT

Quoting Tommy Kahn <>:

> I am attempting to use the Ionize software as described here:
> 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 S. Henriques e-mail:
Investigadora Auxiliar

Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA Portugal

Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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