Re: [AMBER] Atom type of Calcium

From: Bill Ross <>
Date: Mon, 11 Feb 2019 23:37:28 -0800

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.


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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Received on Tue Feb 12 2019 - 00:00:02 PST
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