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 <mgler...@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.mal...@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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