Re: [AMBER] Atom type of Calcium

From: David Case <>
Date: Tue, 12 Feb 2019 14:26:18 +0000

On Tue, Feb 12, 2019, Sunita Patel wrote:

>Can you please provide some links. I was thinking it would be straight
>forward like protein atom types.

It *is* straightforward, although I agree that the manual section on
ions is more complex than it needs to be. Once you select a water model
(via "source leaprc.water.xxxx"), monoatomic ions for that model are
automatically loaded as well. The exact parameters used are printed to
the screen when you load a water file.

You can use the "desc" command in tleap to see which ions are present.
Following the PDB standard, the residue and atom name for calcium2+ are
both "CA". So make sure your input PDB file labels calcium as CA, and you
should be fine.

[Aside: the ff99SB force field is way out of date. If you are not using
AmberTools18, you should upgrade to that version, and use ff14SB for

[Aside to developers: the "Ions" section of the Reference Manual is
written only for some hypothetical super-expert who wants to know
details of ion parameters we no longer use. Can someone add an opening
paragraph describing what users are actually supposed to do in practice,
i.e. that the water leaprc files include ions, and that the recommended
parameters are indentified there?]

...good luck....dac

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Received on Tue Feb 12 2019 - 06:30:03 PST
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