In such situations, you probably need to fall back on running APBS manually via the command line (project home:  Unfortunately, the PyMOL APBS plugin is only able to handle near-perfect input structures.  However, once you can successfully compute a DX file using APBS, then PyMOL can be of use in visualizing the results.

From: LOPES Anne []
Sent: Mon 2/23/2009 9:50 AM
Subject: [PyMOL] error with the APBS plugin


I'm trying to use the APBS plugin to evaluate the electrostatic properties of my protein.
On the one hand, I've have this error:
 Unable to assign parameters for the 1 atom in selection 'unassigned'. Please either remove
 thes unassigned atoms and re-start the calculation or fix their parameters in the generated PQR
 file and run the calculation using the modified PQR file (select 'Use another PQR' in 'Main')

I tried to remove the selection but it seems that the atom in the selection has not been
removed and I still obtain the same error message.

Thus, I tried to edit the PQR file and I removed the atom in the PQR file but in this case I obtain
a new error message:

 Reading PQR-format atom data from /home/Models/pymol-generated.pqr.
 Vio_ctor2: some error occurred.
 Vio_ctor: Vio_ctor2() failed.
 Problem opening virtual socket /home/Models/pymol-generated.pqr!
 Error reading molecules!
 ObjectMapLoadDXFile-Error: Unable to open file!

could you explain the problem to me?
thank you for your help,

best regards,

Anne L

Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
PyMOL-users mailing list