Of course I can, but the only way to do that is to capture the pdb2gmx or grompp output as it seems...<br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">Florian Haberl</b> <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de">
Florian.Haberl@chemie.uni-erlangen.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">hi,<br><br>On Wednesday 21 December 2005 17:53, Tamas Horvath wrote:
<br>> The thing is, I'm working with literally thousands of proteins, and running<br>> some basic simulations on them. Therefore I need to run these simulations<br>> using scripts, so I guess u can't expect me to know every charge
<br>> distribution... These simulations may well be worthless and bogus, but I try<br>> to do my best to make them meaningful...<br><br>you can change your script so it can automatically neutralise your systems.<br>
<br><br><br>><br>> On 12/21/05, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>> ><br>> > Tamas Horvath wrote:<br>> > > I have a protein in water system. The protein has some charge, which I
<br>> > > want to neutralise, introducing stochastic ammount of K+ or Cl-. As far<br>> > > as I figured out, the best way to do it is to use genion. Only I don't<br>> > > know beforehand what the protein's charge would be, so I'm wondering if
<br>> > > it's possible to tell genion to neutralise the system?<br>> ><br>> > Not knowing the pattern of charge distribution in your protein, and thus<br>> > the net charge, sounds to me like a great way to run the risk of doing
<br>> > some worthless simulations and/or bogus science for want of a few<br>> > minutes of observation and thought. I'd call the gromacs utility<br>> > programs' inability to automatically neutralise a system a feature, not
<br>> > a bug!<br>> ><br>> > Cheers,<br>> ><br>> > Mark Abraham<br>> > _______________________________________________<br>> > gmx-users mailing list<br>> > <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > Please don't post (un)subscribe requests to the list. Use the
<br>> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> ><br>><br><br>Greetings,<br><br>Florian<br><br>--<br>-------------------------------------------------------------------------------
<br> Florian Haberl<br> Computer-Chemie-Centrum<br> Universitaet Erlangen/ Nuernberg<br> Naegelsbachstr 25<br> D-91052 Erlangen<br> Mailto: florian.haberl AT <a href="http://chemie.uni-erlangen.de">chemie.uni-erlangen.de</a>
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