Anne, In such situations, you probably need to fall back on running APBS manually via the command line (project home: http://apbs.sourceforge.net). 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. Cheers, Warren
________________________________ From: LOPES Anne [mailto:anne.lo...@cea.fr] Sent: Mon 2/23/2009 9:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] error with the APBS plugin Hello, 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 http://p.sf.net/sfu/XcvMzF8H _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
