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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