Can you please provide some links. I was thinking it would be straight
forward like protein atom types.
Your help will be highly appreciated.
On Tue, Feb 12, 2019 at 1:12 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> Search on the web for calcium residue models (1-atom of course :-) for
> your C0 residue, which will assign an atom type.
>
> 'amber calcium ion' could get you started. You will want to
> compare/contrast how the ion is handled in different environments, and
> be able to defend your choices.
>
> Bill
>
> On 2/11/19 11:22 PM, Sunita Patel wrote:
> > Dear Amber users,
> > I am trying to simulate a calcium binding protein with bound calcium.
> > ff99SB force field am using for that. At the first step itself, am
> getting
> > following error. Although, I specified the correct atom type for calcium
> > ions, still it is unable to recognize it.
> >
> > Please advise how to counteract the problem. I need the solution
> urgently.
> >
> > Please help me. Thanks for the help.
> >
> > With best regards,
> > Sunita
> >
> >
> > ===================
> > WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
> > FATAL: Atom .R<Ca 92>.A<C0 1> does not have a type.
> > FATAL: Atom .R<Ca 93>.A<C0 1> does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> > Quit
> > ===================
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> >
>
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Received on Tue Feb 12 2019 - 00:00:02 PST
