VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 28 2014 - 15:40:44 CDT

Sounds like the mol2 file doesn't get you charge information, so you're
either going to load a file that does contain charges, set the per-atom
partial charges yourself via scripting, or else use an external utility
or script to assign them if you don't have them assigned otherwise.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 28, 2014 at 10:32:57PM +0200, Jean-Patrick Francoia wrote:
> It says 179 atoms. And there are 179 atoms in the molecule.
> I would normaly expect 9.
>
> So that is the issue. How can I assign charges to the (good) atoms ?
>
> Le 28/08/2014 22:31, John Stone a écrit :
> >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...
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >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:
> >>https://www.dropbox.com/s/nl6lq9ow5exo8dw/G1_min.mol2?dl=0) 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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/