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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
43 stars 15 forks source link

running error #43

Open chaoyangma24 opened 1 year ago

chaoyangma24 commented 1 year ago

Thank for your ProtoCaller. When I run python T4-lysozyme.py, there appears the following wrongs. Your reply would be very appreciated. WARNING:openff.toolkit.utils.toolkit_registry:Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. INFO:numexpr.utils:Note: detected 72 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable. INFO:numexpr.utils:Note: NumExpr detected 72 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. INFO:numexpr.utils:NumExpr defaulting to 8 threads. WARNING:pymbar.timeseries:Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data. INFO:pymbar.mbar_solvers:JAX detected. Using JAX acceleration. /home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/Sire/init.py:278: DeprecationWarning: dist() and linux_distribution() functions are deprecated in Python 3.5 ld = _pf.linux_distribution() INFO:root:Downloading ligand files from the Protein Data Bank... INFO:root:Running OpenBabel... INFO:root:Running obminimize... INFO:root:Running OpenBabel... INFO:root:Running obminimize... /home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/Bio/Seq.py:1756: BiopythonDeprecationWarning: myseq.tomutable() is deprecated; please use MutableSeq(myseq) instead. BiopythonDeprecationWarning, INFO:root:Running PDB2PQR... INFO:root:Running OpenBabel... INFO:root:Parametrising original crystal system... INFO:root:Running tleap... INFO:root:Running tleap... INFO:root:Running tleap... INFO:root:Parametrising ligand benzol... WARNING:root:Cannot parametrise unprotonated ligand. Protonating first with default parameters... INFO:root:Running OpenBabel... INFO:root:Running OpenBabel... INFO:root:Running antechamber... INFO:root:Running parmchk2... INFO:root:Running tleap... INFO:root:Parametrising ligand o-xylene... WARNING:root:Cannot parametrise unprotonated ligand. Protonating first with default parameters... INFO:root:Running OpenBabel... INFO:root:Running OpenBabel... INFO:root:Running antechamber... INFO:root:Running parmchk2... INFO:root:Running tleap... INFO:root:Creating morph benzol~o-xylene... /home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/ProtoCaller/Wrappers/rdkitwrapper.py:1468: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead. mcs_string = _MCS.FindMCS(*args, *kwargs).smarts /home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/ProtoCaller/Wrappers/rdkitwrapper.py:1468: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead. mcs_string = _MCS.FindMCS(args, **kwargs).smarts INFO:root:Solvating... Traceback (most recent call last): File "T4-lysozyme.py", line 34, in system.prepareComplexes() File "/home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/ProtoCaller/Ensemble/init.py", line 240, in prepareComplexes centre=self.centre, work_dir=curdir.path, filebase="complex")] File "/home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/ProtoCaller/Solvate/init.py", line 84, in solvate files = _PC.IO.GROMACS.saveAsGromacs(filebase, complex) File "/home/chaoyang/miniconda3/envs/protocaller/lib/python3.7/site-packages/ProtoCaller/IO/GROMACS.py", line 33, in saveAsGromacs _pmd.load_file(filebase + ".gro87").save(filebase + ".gro", combine="all") File "/home/chaoyang/soft/amber22/lib/python3.9/site-packages/parmed/formats/registry.py", line 168, in load_file raise FileNotFoundError('%s does not exist' % filename) FileNotFoundError: complex.gro87 does not exist