This is a subset of the directory structure used to run Phenix-Amber refinements. Currently, it has the log files and a script to catalogue the errors.
python catalogue_errors.py
ends with
- (2) adjust atom valence penalty parameters in APS.DAT, and/or 9 ['1pge', '3nxu', '1cx2', '2pcb', '1w0e', '3nt1', '2b4z', '1ue8', '3b4x']
- Check contents of "leap.log" 3 ['3ipq', '1jkx', '1fvv']
- 3ipq: resname is a number? 'HET 965 A 801 41'
- IndexError: list index out of range 15 ['2jlq', '2wn9', '2w8c', '1nsk', '1gvd', '2vc2', '2uyz', '2xbm', '2xeg', '2xb4']
- This is probably limitation in pdb4amber (new code) in detecting gap.
- Molecule too small to optimise 2 ['1rer', '1io4']
- OSError: [Errno 2] No such file or directory 1 ['3ll8']
- Running elbow/antechamber for MSE 16 ['1fg5', '2jla', '2g3k', '2dwk', '1t6i', '1xm3', '1vjl', '2cy2', '1i6k', '2axy']
- Sorry: Output file is empty : 51 ['3cfb', '1c0n', '1qf6', '3lkz', '3n9g', '3hww', '1brr', '2br7', '3fg1', '2rg3']
- ValueError: invalid literal for int() with base 16: 2 ['2b9v', '1fnt']
- assert (ero.return_code == 0) 8 ['3hsh', '3bwu', '2zhx', '3oiu', '3gj0', '1fss', '3ous', '1baw']
- may be due to minimization step (e.g: 3hsh, 2zhx)
- assert 0 1 ['1cb6']
- this is due to there not being a valid MTZ file for phenix.refine, AmberPrep runs fine
- in judgebondtype() of antechamber.c properly, exit 6 ['2ayl', '2onk', '2j6e', '3od5', '3cij', '1zv8']
- not finished 3 ['2ger', '2f8x', '2izz']
- phenix.refine seems to be failing but AmberPrep is OK. Will delve deeper. NWM
- For 2iZZ, the refinement fails with large gradient if the input model is take from the PDB but is fine if minimize=amber_h is used in AmberPrep
- of bcc() in charge.c properly, exit 7 ['2q3z', '1ihi', '3oha', '3gug', '3o41', '2r8j', '3lex']
- phenix.refine running/done 237 ['3kqr', '2bky', '1ar2', '2gps', '1xni', '1a9b', '1wmk', '3f6l', '2c6q', '3g4z']
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