Error in running input file and trajectory analysis #116
Description
Hi,
I am facing error in running the input file. When using the option to Save simulation setup as XML files and running the prepared python script, it gives error:
"openmmdl_simulation -t protein-processed_openMMDL.pdb -s OpenMMDL_Simulation.py -l Ligand.sdf -f run
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/gsk/.local/lib/python3.10/site-packages/Bio/Application/init.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.
We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
Preparing MD Simulation with ligand
Adding hydrogens
Forcefield and Water Model Selected
Complex topology has 4032 atoms.
Protein with buffer solvent prepared
Building system...
Traceback (most recent call last):
File "/home/gsk/Downloads/openmmdl-testrun/openmmdl_simulation/New-run/openmmdl_simulation/run/OpenMMDL_Simulation.py", line 137, in
file.write(XmlSerializer.serialize(system))
NameError: name 'XmlSerializer' is not defined"
When not saving the XML file and running, it runs fine but gives error during trajectory analysis:
Traceback (most recent call last):
File "/home/gsk/Downloads/openmmdl-testrun/openmmdl_simulation/New-run/noxml-openmmdl_simulation/run/OpenMMDL_Simulation.py", line 162, in
mdtraj_conversion(f'Equilibration_{protein}', 'mdtraj_pdb_dcd')
File "/home/gsk/anaconda3/envs/openmmdl/lib/python3.10/site-packages/openmmdl/openmmdl_simulation/scripts/post_md_conversions.py", line 17, in mdtraj_conversion
mdtraj_frames = md.load_dcd("trajectory.dcd", top=pdb_file)
File "mdtraj/formats/dcd/dcd.pyx", line 162, in mdtraj.formats.dcd.load_dcd
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/core/trajectory.py", line 170, in _parse_topology
_traj = load_frame(top, 0, **kwargs)
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/core/trajectory.py", line 313, in load_frame
return loader(filename, frame=index, **kwargs)
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbfile.py", line 152, in load_pdb
with PDBTrajectoryFile(filename, standard_names=standard_names, top=top) as f:
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbfile.py", line 292, in init
self._read_models()
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbfile.py", line 624, in _read_models
pdb = PdbStructure(self._file, load_all_models=True)
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbstructure.py", line 283, in init
self._load(input_stream)
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbstructure.py", line 299, in _load
self._add_atom(Atom(pdb_line, self))
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbstructure.py", line 875, in init
self.residue_number = _read_residue_number(pdb_line[22:26], pdbstructure, self)
File "/home/gsk/.local/lib/python3.10/site-packages/mdtraj/formats/pdb/pdbstructure.py", line 138, in _read_residue_number
return int(num_str)
ValueError: invalid literal for int() with base 10: 'A001'
"