Hi Andrew.

I experienced something similar for the autodock_plugin.
http://www.pymolwiki.org/index.php/Autodock_plugin

During my trials, I notified two things for autodock.
It did not like "funny atom names" or "Alternative configuration"

Could this be a case for your protein / ligand?
I don't know if is the same for the APBS plugin, but you could try?
http://www.pymolwiki.org/index.php/Autodock_plugin#Example_1_-_Rename_of_funny_atom_names

Some of the "preparation" scripts for both plugins are coming from the same research groups.
I think they both use: pdb2pqr or something.

Best
Troels

2011/12/7 Michael Lerner <mglerner@gmail.com>
Hi Andrew,

The main limitation for problems like this is that you need to have
parameters for the ligand. Making sure that you have "good" parameters
is often an expert-level topic, and you're probably best served by the
APBS or PDB2PQR listservs as well as the literature ... but, you can
get a decent start on things with PDB2PQR itself. See
http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization
for some good starting instructions. Once you have a PQR file that
includes both the protein and the ligand, the PyMOL/APBS plugin should
do everything that you need.

If that doesn't solve your problem, please let me know.

Cheers,
-Michael

On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew
<Andrew.Malaby@umassmed.edu> wrote:
> Hey guys,
>
> I am trying to calculate electrostatics with a ligand bound to my molecule using ABPS.  I am not having success.  Everything I've read seems to say that this is a normal limitation with APBS, and I've tried other programs to no avail.  I have not been able to rebuild my molecule in the "correct format" either.  Any help here is greatly appreciated.
>
> Andrew
> UMass Med School, Worcester, MA
>
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--
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN   47374-4095

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