VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 08 2008 - 22:55:36 CDT

Hi,
  I'm assuming that you've got no charges in VMD since you're just
loading a PDB file by itself.

You'll want to load a PSF with your PDB, or else run autopsf on
it before running the get_total_charge script as VMD doesn't automatically
assign this kind of information if it's not otherwise present.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 08, 2008 at 11:17:33PM -0400, MIke S wrote:
> Hello there,
>
> First of all, thank you to whoever maintains this mailing list, 'cause
> as a VMD/NAMD newbie it's definitely helped me out.
>
> So, I've been trying to figure out the charge state of my molecule
> using the 'get_total_charge' script and a suggestion I found on this
> site
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4703.html),
> but neither has worked for me. I checked the VMD manual and may have
> overlooked it, but I can't find the solution.
>
> Here is some relevant info:
>
> I think 've processed the get_total_charge script correctly using the
> VMD TkConsole, because I ran the get_total_mass script (which is very
> similar to the charge one) and it worked. I've posted the results of
> the command lines below.
>
> For the scripts:
> ____________
> vmd > get_total_mass
> 16682.0338011
> vmd > get_total_charge
> 0.0
>
> For the suggestions:
> _____________
> vmd > set everyone [atomselect top all]
> atomselect9
> vmd > set protein [atomselect top protein]
> atomselect10
> vmd > puts " TOTAL CHARGE ON THE SYSTEM: [eval vecadd [$everyone get charge]]"
> vmd > puts "TOTAL CHARGE ON THE PROTEIN: [eval vecadd [$protein get charge]]"
> vmd > $everyone delete
> vmd > $protein delete
> vmd >
>
> I know that my protein is charged, because I checked the same PDB file
> on another program and the charge is -23. I would prefer to use VMD
> over my other program. I've also tried the script on other proteins
> and the charge comes up as 0 as well.
>
> In case it makes a difference, I'm running VMD on a PowerPc Mac.
>
> Thanks for any and all suggestions.
>
> Cheers,
>
> Mike 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078