From: John Stone (
Date: Thu Aug 28 2014 - 15:31:34 CDT

The warning comes from some parts of your structure not having
charges assigned in the input files that VMD (and later APBS) are
being provided. One way to check how many atoms lack charge in VMD
is do to something like this:
  set sel [atomselect top "charge == 0"]
  $sel num

That will tell you how many atoms are uncharged...

  John Stone

On Thu, Aug 28, 2014 at 10:00:58PM +0200, Jean-Patrick Francoia wrote:
> Hello,
> I have created an octapeptide of lysine (see mol2 file attached:
> with a
> certain manner.
> I then "minimized" the structure with Spartan. That's a rough (and
> probably wrong) minimization, but I just need an idea of the 3D
> structure of my molecule. (Please do not focus on this part, this
> molecule is only an example, and the way I build it cannot be changed).
> Finally, I would like to create an electrostatic potential map for this
> molecule. The matter is APBS tells me my molecule is not charged. I
> would like to understand why it keeps telling me that.
> I have some -NH3+ functions on my molecule (8 to be correct), and one
> carboxylic acid deprotonated. So the charge should be 7.
> Maybe it is because the structure is correct, but the charge of each
> atom is not reported in a mol2 file ?
> I would like to understand what the problem is, and find a way to
> correct it. Could you give me a hand ?
> Sincerely

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349