Hi there, I'm running into a few errors when using the "Calculate Protein Ionization and Residue pK..." protocol.

The first error occurs with the PDB file 3GHG, which has the following in its Output.log:

[2011-06-14 11:32:25] ------------------------------------

[2011-06-14 11:32:25] Protocol Name = 'Calculate Protein Ionization and Residue pK'

[2011-06-14 11:32:25] User Name = 'oyuifi'

[2011-06-14 11:32:25] Run ID = '{947D06EF-CDC6-4A4D-AAC0-09622F1AA305}'

[2011-06-14 11:32:25] Client message: 'step 1/2:3GHG'

[2011-06-14 11:32:49] The results may be affected by the following imperfections in the input structure:Missing Residues (shown in lower case) :

[2011-06-14 11:33:09] Client message: 'Running forcefield tools...'

[2011-06-14 11:33:09] Started running 'ForcefieldTool'

[2011-06-14 11:33:34] Finished running 'ForcefieldTool'

[2011-06-14 11:33:34] Client message: 'ForcefieldTool finished successfully.'

[2011-06-14 11:33:38] Started running '3GHG'

[2011-06-14 12:15:48] Finished running '3GHG'

[2011-06-14 12:15:49] Client message: 'GBpK running'

[2011-06-14 12:15:49] Started running 'GBpK'

[2011-06-14 12:25:45] Finished running 'GBpK'

[2011-06-14 12:25:45] Client message: 'GBpK finished successfully.'

[2011-06-14 12:25:45] Client message: 'CreateGBpK finished'

[2011-06-14 12:25:45] Client message: 'pK calculations...'

[2011-06-14 12:25:45] Started running 'PHPK'

[2011-06-14 12:26:06] Finished running 'PHPK'

[2011-06-14 12:26:06] Client message: 'PHPK finished successfully.'

[2011-06-14 12:26:06] Client message: 'Finished: 3GHG '

[2011-06-14 12:26:06] Client message: 'reference pK calculations...'

[2011-06-14 12:26:06] Started running 'PHPK'

[2011-06-14 12:26:19] Finished running 'PHPK'

[2011-06-14 12:26:19] Client message: '3GHG_0 finished successfully.'

[2011-06-14 12:26:30] Client message: 'Finished: 3GHG '

[2011-06-14 12:26:30] Client message: 'Annotate MacroMolecule...'

[2011-06-14 12:26:33] Client message: 'Finished: Ionize '

[2011-06-14 12:26:33] Client message: 'CHARMm protonate...'

[2011-06-14 12:26:33] Started running 'RunCHARMm'

[2011-06-14 12:31:27] Finished running 'RunCHARMm'

[2011-06-14 12:32:18] [ERROR] Open coordinate file C:/Program Files (x86)/Accelrys/Discovery Studio 3.0/PipelinePilot/web/jobs/oyuifi/{947D06EF-CDC6-4A4D-AAC0-09622F1AA305}/Intermediate/3GHG.reprot.crd failed

[2011-06-14 12:32:19] [ERROR] Failed to protonate protein.

[2011-06-14 12:32:19] Client message: 'Failed to protonate protein.'

[2011-06-14 12:32:19] Client message: 'Failed:3GHG'

[2011-06-14 12:32:19] Final message: 'Failed:3GHG'

The second is with a custom PDB file of ferritin (attached). I get this error when I try to run the same protocol on it:

[2011-06-14 12:40:10] ------------------------------------

[2011-06-14 12:40:10] Protocol Name = 'Calculate Protein Ionization and Residue pK'

[2011-06-14 12:40:10] User Name = 'oyuifi'

[2011-06-14 12:40:10] Run ID = '{04850850-6EC3-401A-98D5-ED6C0EC059A3}'

[2011-06-14 12:40:10] Client message: 'step 1/2:24mer-fer0'

[2011-06-14 12:40:37] The results may be affected by the following imperfections in the input structure:Missing Residues (shown in lower case) :

[2011-06-14 12:41:07] Client message: 'Running forcefield tools...'

[2011-06-14 12:41:07] Started running 'ForcefieldTool'

[2011-06-14 12:41:38] Finished running 'ForcefieldTool'

[2011-06-14 12:41:38] Client message: 'ForcefieldTool finished successfully.'

[2011-06-14 12:41:44] Started running '24mer-fer0'

[2011-06-14 13:40:13] Finished running '24mer-fer0'

[2011-06-14 13:40:14] Client message: 'GBpK running'

[2011-06-14 13:40:14] Started running 'GBpK'

[2011-06-14 13:40:17] Finished running 'GBpK'

[2011-06-14 13:40:17] Client message: 'GBpK finished successfully.'

[2011-06-14 13:40:17] Client message: 'CreateGBpK finished'

[2011-06-14 13:40:18] [ERROR] Failed to calculate ionization properties.

[2011-06-14 13:40:18] Client message: 'Failed to calculate ionization properties.'

[2011-06-14 13:40:18] Client message: 'Failed:24mer-fer0'

[2011-06-14 13:40:18] Final message: 'Failed:24mer-fer0'

Any ideas? I'm running DS 3.0.0.10321 on Windows 7 x64 with 8-core Intel Xeons and 12 GB of RAM.