VMD-L Mailing List
From: MIke S (vmd.namd_at_gmail.com)
Date: Thu May 08 2008 - 22:17:33 CDT
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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
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