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
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
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
