So, the bottomline is, that I have to capture e.g. the grompp output to determine the net charge?<br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">Tamas Horvath</b> <<a href="mailto:hotafin@gmail.com">
hotafin@gmail.com</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;">Thanks Alan, so the mysterious 2nd protein is indeed the new ions :)
<div><span class="e" id="q_1084e099845567b9_1"><br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">Alan Dodd</b> <<a href="mailto:anoddlad@yahoo.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
anoddlad@yahoo.com</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;">Discovering the protein's charge is pretty trivial -<br>many programs in gromacs will give an error message
<br>for systems with a net charge, eg. pdb2gmx and of<br>course grompp. As you've got to run grompp for genion<br>anyways, just do that and pay attention to the output.<br> Ions are given a seperate group in the topology and
<br>.mdp files, as if they were a separate protein.<br>You'll have to fix these parts yourself.<br><br>--- Tamas Horvath <<a href="mailto:hotafin@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
hotafin@gmail.com</a>> wrote:<br><br>> I have a protein in water system. The protein has
<br>> some charge, which I want<br>> to neutralise, introducing stochastic ammount of K+<br>> or Cl-. As far as I<br>> figured out, the best way to do it is to use genion.<br>> Only I don't know<br>> beforehand what the protein's charge would be, so
<br>> I'm wondering if it's<br>> possible to tell genion to neutralise the system?<br>><br>> 2nd.: If genion puts some ions in the system, are<br>> the ions considered as a<br>> 2nd protein?<br>><br>
> Hota
<br>><br>> On 12/21/05, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">tsjerkw@gmail.com</a>><br>> wrote:<br>> ><br>> > Hi Tamas,
<br>> ><br>> > You have to specify it yourself.
<br>> ><br>> > Cheers,<br>> ><br>> > Tsjerk<br>> ><br>> > On 12/20/05, Tamas Horvath <<a href="mailto:hotafin@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
hotafin@gmail.com</a>><br>> wrote:<br>> > ><br>
> > > I want to neutralise my system (chargewise), so<br>> I use genion for that.<br>> > > Do I always have to specify the number of ions<br>> to use, or is there a way<br>> > > to automatically neutralise the system?
<br>> > ><br>> > > _______________________________________________<br>> > > gmx-users mailing list<br>> > > <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org</a><br>> > >
<br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > > Please don't post (un)subscribe requests to the
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<br>> > --<br>> ><br>> > Tsjerk A. Wassenaar, M.Sc.
<br>> > Groningen Biomolecular Sciences and Biotechnology<br>> Institute (GBB)<br>> > Dept. of Biophysical Chemistry<br>> > University of Groningen<br>> > Nijenborgh 4<br>> > 9747AG Groningen, The Netherlands
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