Hello all, I'm running incentive pymol 1.7.4 on Windoze 7 64bit professional. The APBS plugin fails with; below is the output.
Temp file locations are standard: Temp PQR: C:\Users\mheller\AppData\Local\Temp\pymol-generated.pqr Temp PDB: C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb Temp DX: C:\Users\mheller\AppData\Local\Temp\pymol-generated.dx APBS input: C:\Users\mheller\AppData\Local\Temp\pymol-generated.in I'm confused that's it's searching for C:\Users\mheller\AppData\Local\Temp\pymol-generated-PE0.dx ... Any ideas what's going? Thanks Markus Erasing contents of C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb in order to generate new PDB file -------------------------- PDB2PQR - a Python-based structural conversion utility -------------------------- Please cite your use of PDB2PQR as: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). APBS's psize.py was used to calculated grid dimensions Estimated memory usage 2658.73432159 MB out of maximum allowed 1500.0 Maximum memory usage exceeded. Old grid dimensions were [193, 321, 225] Fine grid points rounded down from [159, 265, 185] New grid dimensions are [129, 257, 161] APBS Tools: coarse grid: (127.315,236.083,151.276) APBS Tools: fine grid: (94.891,158.872,108.986) APBS Tools: center: (5.999,31.917,23.462) APBS Tools: fine grid points (129,257,161) Getting APBS input Erasing contents of C:\Users\mheller\AppData\Local\Temp\pymol-generated.in in order to write new input file Erasing contents of C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb in order to generate new PDB file -------------------------- PDB2PQR - a Python-based structural conversion utility -------------------------- Please cite your use of PDB2PQR as: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). Could not find C:\Users\mheller\AppData\Local\Temp\pymol-generated.dx so searching for C:\Users\mheller\AppData\Local\Temp\pymol-generated-PE0.dx ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'C:\Users\mheller\AppData\Local\Temp\pymol-generated-PE0.dx' exist? -- Markus Heller, Ph.D. Senior Scientist, NMR CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
