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.
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...
> > John Stone
> > vmd_at_ks.uiuc.edu
> >On Thu, Aug 28, 2014 at 10:00:58PM +0200, Jean-Patrick Francoia wrote:
> >>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 ?
-- 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/