VMD-L Mailing List
From: DimitryASuplatov (genesup_at_gmail.com)
Date: Mon Apr 27 2009 - 04:43:34 CDT
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Hello,
I want to calculate net system charge of my system given pdb and psf
files. I also want to be able to do it automatically via script.
I tried using something like:
mol load psf $fname.psf pdb $fname.pdb
set ev [atomselect top all]
set indices [$ev get index]
set netcharge 0
foreach ind $indices {
set at [atomselect top "index $ind"]
set charge [$at get charge]
set netcharge [ expr $netcharge + $charge ]
$charge delete
}
puts "$netcharge"
It works and outputs the correct value though it works some 5-10
seconds compared to autoioize plugin which does the complete job
including ionization in less then 5 seconds.
So my question is
Is there a one-word command to quickly
calculate system net charge give charmm topology and pdb coordinates?
Thank you for your time.
SDA
- Next message: Athanassios Stavrakoudis: "Re: Calculating system net charge with tcl in VMD"
- Previous message: John Stone: "Re: RMSD of a protein shell, from the NAMD traj"
- Next in thread: Athanassios Stavrakoudis: "Re: Calculating system net charge with tcl in VMD"
- Reply: Athanassios Stavrakoudis: "Re: Calculating system net charge with tcl in VMD"
- Reply: Peter Freddolino: "Re: Calculating system net charge with tcl in VMD"
- Reply: Eduardo Cruz-Chu: "Re: Calculating system net charge with tcl in VMD"
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