[gmx-users] genion

[Tamas Horvath]

On 12/21/05, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
>
> hi
>
> On Wednesday 21 December 2005 16:26, Tamas Horvath 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?
>
> look at grompp output, theres somewhere charge of the system.


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...

>
> > 2nd.: If genion puts some ions in the system, are the ions considered as
> a
> > 2nd protein?
> >
>
> no you have to add them to your topol.top file manually and also if you
> use
> t/p couple you have to add them to your mdp file.


After genion I run pdb2gmx & grompp...
The new .top file looks like this :

; Include chain topologies
#include "/home/hota/jbproject/data/work/1BTK_Y40N_A.itp"
#include "/home/hota/jbproject/data/work/1BTK_Y40N_B.itp"

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL              5417

**********************
In this case there are 5 Cl- ions (named "CL-") added to the system

> 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?
> > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > > --
> > >
> > > 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
> > >
> > > _______________________________________________
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> > >
> >
> greetings,
>
> florian
>
>
> --
>
> -------------------------------------------------------------------------------
> Florian Haberl
> Computer-Chemie-Centrum
> Universitaet Erlangen/ Nuernberg
> Naegelsbachstr 25
> D-91052 Erlangen
> Mailto: florian.haberl AT chemie.uni-erlangen.de
>
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