I was doing it just to make sure the total charge is zero.
On Tue, Sep 11, 2012 at 2:03 PM, Carmenza Martinez <crm3680.gmail.com>wrote:
> one simple question...do you absolutely need to add ions? Sometimes adding
> ions can be troublesome and cause instability to the simulation. Are you
> only doing it just to make sure that the "unperturbed charge of the unit"
> is zero? or is it something that your simulation must have in order to
> answer your question...
>
>
> On Tue, Sep 11, 2012 at 1:43 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > I'm having trouble adding ions.
> >
> > Here is what I did
> >
> > edited pdb.
> > loaded into xleap (leap added a missing atom and H's)
> > saveoff .lib
> > saveoff .pdb
> > saveamberparm pdb .prmtop .inpcrd
> >
> > and I get:
> >
> > WARNING: The unperturbed charge of the unit: -3.000000 is not zero.
> >
> > (files were created)
> >
> > therefore I tried adions pdb Na+ 0
> > (argument #1 is a type string unit)
> >
> > am1=createUnit pdb
> >
> > addions am1 Na+ 0
> > Na+ has a charge of 0.
> > addIons: Can't neutralize.
> >
> > from what i understand I created a unit and tried to neutralize, but...
> no
> > bueno. The endgame is to do a simple minimization of this protein.
> > any suggestions on how to get un-stuck?
> >
> > Thanks and sorry for the simplicity of the question. I did search the
> > archives and tutorials, but I'm a bit lost. I'm missing something
> simple.
> >
> > Jonathan
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Carmenza Martinez
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>
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Received on Tue Sep 11 2012 - 11:30:04 PDT
