patrickbryant1
commented
2 weeks ago Hi,
It seems that you are missing files here. Make sure all the predictions are generated before proceeding to the next step.
Closed Dong-HoSeo closed 1 week ago
patrickbryant1
commented
2 weeks ago Hi,
It seems that you are missing files here. Make sure all the predictions are generated before proceeding to the next step.
Source 'gaff-2.11' could not be read. If this is a file, ensure that the path is correct. Looked in the following paths and found no files named 'gaff-2.11': /home/dhseo/Data_HDD2/Umol /home/dhseo/mambaforge/envs/umol/lib/python3.12/site-packages/openff/amber_ff_ports/offxml /home/dhseo/mambaforge/envs/umol/lib/python3.12/site-packages/smirnoff99frosst/offxml /home/dhseo/mambaforge/envs/umol/lib/python3.12/site-packages/openforcefields/offxml If 'gaff-2.11' is present as a file, ensure it is in a known SMIRNOFF encoding. Valid formats are: ['XML'] Parsing failed while trying to parse source as a file with the following exception and message: <class 'openff.toolkit.utils.exceptions.SMIRNOFFParseError'> syntax error: line 1, column 0
Traceback (most recent call last): File "/home/dhseo/Data_HDD2/Umol/./src/relax/openmm_relax.py", line 180, in
system_generator = SystemGenerator(
^^^^^^^^^^^^^^^^
File "/home/dhseo/mambaforge/envs/umol/lib/python3.12/site-packages/openmmforcefields/generators/system_generators.py", line 269, in init
raise GAFFNotSupportedError(
openmmforcefields.generators.template_generators.GAFFNotSupportedError: This release (0.13.x) of openmmforcefields temporarily drops GAFF support and thereby the GAFFTemplateGenerator class. Support will be re-introduced in future releases (0.14.x). To use this class, install version 0.12.0 or older.
/home/dhseo/mambaforge/envs/umol/lib/python3.12/site-packages/Bio/PDB/PDBParser.py:395: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 1249
warnings.warn(
Traceback (most recent call last):
File "/home/dhseo/Data_HDD2/Umol/./src/relax/add_plddt_to_relaxed.py", line 111, in
relaxed_coords, relaxed_chains, relaxed_atom_numbers, relaxed_3seq, relaxed_resnos, relaxed_atoms, relaxed_bfactors = read_pdb(args.relaxed_complex[0])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dhseo/Data_HDD2/Umol/./src/relax/add_plddt_to_relaxed.py", line 28, in read_pdb
f=open(pdbname,'rt')
^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: './data/test_case/7NB4//7NB4_relaxed_complex.pdb'
The final relaxed structure can be found at ./data/test_case/7NB4//7NB4'_relaxed_plddt.pdb'