<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 16:26, Tamas Horvath wrote:<br>> I have a protein in water system. The protein has some charge, which I want<br>> to neutralise, introducing stochastic ammount of K+ or Cl-. As far as I
<br>> figured out, the best way to do it is to use genion. Only I don't know<br>> beforehand what the protein's charge would be, so I'm wondering if it's<br>> possible to tell genion to neutralise the system?<br>
<br>look at grompp output, theres somewhere charge of the system.</blockquote><div><br>The case is not that easy since I run things using a script... but if it cannot be done automatically, then I could always capture the output... but I rather not...
<br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">><br>> 2nd.: If genion puts some ions in the system, are the ions considered as a
<br>> 2nd protein?<br>><br><br>no you have to add them to your topol.top file manually and also if you use<br>t/p couple you have to add them to your mdp file.</blockquote><div><br>After genion I run pdb2gmx & grompp...
<br>The new .top file looks like this :<br><br>; Include chain topologies<br>#include "/home/hota/jbproject/data/work/1BTK_Y40N_A.itp"<br>#include "/home/hota/jbproject/data/work/1BTK_Y40N_B.itp"<br><br>
; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000
<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1
<br>SOL 5417<br><br>**********************<br>In this case there are 5 Cl- ions (named "CL-") added to the system<br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> Hota<br>><br>> On 12/21/05, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> 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">hotafin@gmail.com</a>> wrote:<br>> > ><br>> > > I want to neutralise my system (chargewise), so I use genion for that.
<br>> > > Do I always have to specify the number of ions 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">gmx-users@gromacs.org</a><br>> > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
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<br>> > ><br>> ><br>> ><br>> > --<br>> ><br>> > Tsjerk A. Wassenaar, M.Sc.<br>> > Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>> > Dept. of Biophysical Chemistry
<br>> > University of Groningen<br>> > Nijenborgh 4<br>> > 9747AG Groningen, The Netherlands<br>> > +31 50 363 4336<br>> ><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>-------------------------------------------------------------------------------
<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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