[gmx-users] genion

[Alan Dodd]

Discovering the protein's charge is pretty trivial -
many programs in gromacs will give an error message
for systems with a net charge, eg. pdb2gmx and of
course grompp.  As you've got to run grompp for genion
anyways, just do that and pay attention to the output.
 Ions are given a seperate group in the topology and
.mdp files, as if they were a separate protein. 
You'll have to fix these parts yourself.

--- Tamas Horvath <hotafin at gmail.com> wrote:

> I have a protein in water system. The protein has
> some charge, which I want
> to neutralise, introducing stochastic ammount of K+
> or Cl-. As far as I
> figured out, the best way to do it is to use genion.
> Only I don't know
> beforehand what the protein's charge would be, so
> I'm wondering if it's
> possible to tell genion to neutralise the system?
> 
> 2nd.: If genion puts some ions in the system, are
> the ions considered as a
> 2nd protein?
> 
> Hota
> 
> On 12/21/05, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> >
> > Hi Tamas,
> >
> > You have to specify it yourself.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 12/20/05, Tamas Horvath <hotafin at gmail.com>
> wrote:
> > >
> > > I want to neutralise my system (chargewise), so
> I use genion for that.
> > > Do I always have to specify the number of ions
> to use, or is there a way
> > > to automatically neutralise the system?
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > >
> http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the
> list. Use the
> > > www interface or send it to
> gmx-users-request at gromacs.org.
> > >
> > >
> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc.
> > Groningen Biomolecular Sciences and Biotechnology
> Institute (GBB)
> > Dept. of Biophysical Chemistry
> > University of Groningen
> > Nijenborgh 4
> > 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> list. Use the
> > www interface or send it to
> gmx-users-request at gromacs.org.
> >
> >
> > _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
gmx-users-request at gromacs.org.


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com