From: Ajasja Ljubetič (
Date: Fri Jul 12 2013 - 04:53:34 CDT


You (most probably) have a non-integer charge before neutralization. If you
have a total charge of for example of -1.2 there is no possible way to
neutralize this with ions.

You have to figure out why the charge is non-integer. Do you have any
nonstandard residues? Have you changed or created some parameters?


On 12 July 2013 10:21, <> wrote:

> Dear VMD Support Team,
> I’m trying to neutralize a protein structure with 3 chains by using
> autoionize plug-in in VMD.
> Plug-in gives the following message:
> System net charge after adding ions: 0.1800074577331543e.
> As well as an error message occurs on the screen as:
> System has a non-integer total charge. There was a problem in the process
> of building it.
> I know that you have received same question before. I have taken into
> consideration what you suggested. But I do not have atom type longer than 5
> characters in PSF file. Additionally, I should mention that my pdb and psf
> files were also generated by using VMD 1.9.1.
> I would appreciate if you can help me with that problem.
> Best Regards,
> Melis Yıldırım
> MS Student
> Bogazici University Polymer Research Center
> Istanbul / Turkey