very helpful!
On Tue, Sep 11, 2012 at 2:07 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
> Jonathan,
> the syntax for addions command is as follows: addions <model_name> <ion>
> <number of ions>
> The last argument is the number of ions you wish to add, not the desired
> total charge.
>
> In your case, the command will be: addions pdb Na+ 3
>
> Hope it helps
>
> Sasha
>
>
> On 9/11/2012 11:03 AM, Carmenza Martinez 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
> >>
> >
> >
>
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Received on Tue Sep 11 2012 - 11:30:06 PDT
