VMD-L Mailing List

From: MIke S (vmd.namd_at_gmail.com)
Date: Fri May 09 2008 - 00:45:39 CDT

John,

You the man. Your suggestions worked beautifully, and the value is
even more accurate than what I had before. Very cool.

Thanks a million,

Mike

On 5/8/08, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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
>