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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>
--
Carmenza Martinez
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Received on Tue Sep 11 2012 - 11:30:03 PDT
