VMD-L Mailing List

From: melis.yildirim_at_boun.edu.tr
Date: Fri Jul 12 2013 - 03:21:25 CDT

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