[gmx-users] How to get the total charge?

[David]

On Mon, 2003-06-16 at 17:12, TAPO (Thomas Agersten Poulsen) wrote:
> Dear gmx-list.
> 
> 	Given a topology file and an index file, how do I compute to total
> charge of each group in the index file?
> 
> This might be a silly question, but I am sort of new to all these wonderful
> Gromacs tools, so please bear with me :-)

Hm........

There is no direct tool that does it, however you might use 
editconf -f topol.tpr -o q.pdb -n index -grasp

this will give you a pdb file of your selected group with the charge in
the b-factor field. Then a tiny perl script would be able to get the
total charge
#!/usr/bin/perl -w

open(KKK,"grep ATOM q.pdb |") || die("q.pdb");
$qtot = 0;
while ($line = <KKK>) {
  chomp($line);
  @tmpe = split(' ',$line);
  $qtot += $tmp[8];
}
close KKK;
print "qtot = $qtot\n";

(script not tested...)


> 
> Best regards
> Thomas
> 
> Thomas A. Poulsen
> Novozymes A/S
> Novo Alle 1, 2C.S44
> DK-2880 Bagsværd
> +45 44 42 27 23
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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