Re: [PyMOL] APBS with ions

[Thomas H. <th...@th...>]

Hi Kamil,

The "Selection" field uses "polymer & ..." by default, which excludes
ions. You can use a selection which includes ions instead, for example
"all", "not solvent", or something like "(polymer | name CAL) & ...".

Here an example that works for me:

fetch 1rx1
alter elem Ca, resn="CAL"
alter elem Ca, name="CAL"

In the APBS Electrostatics panel, use "(polymer | name CAL) & 1rx1" as
the selection and "--ff=CHARMM" as pdb2pqr command line option.

Hope that helps.

Cheers,
  Thomas

On Mon, Nov 1, 2021 at 9:21 PM Kamil Steczkiewicz
<kam...@gm...> wrote:
>
> Hi,
> How to include Ca/Zn ions when using APBS built into Pymol? I'm switching to CHARMM in command line options; CHARMM has CAL and ZN2 atoms already defined in the DAT file. But there's still no difference in electrostatics maps with and without ions in the structure. Also, the default 'prepared01' object lacks the ions.
> Thanks for any clues,
> Kamil
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