Error at generating template files with peleffy
etiur opened this issue · comments
I was trying to generate a template file for a cofactor, FAD, in 'OPLS2005' using the version of peleffy in this conda envinronment in marenostrum 0
conda activate /gpfs/projects/bsc72/conda_envs/platform/1.6.0
But it gave this error
Traceback (most recent call last):
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/main.py", line 299, in
main(args)
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/main.py", line 283, in main
run_peleffy(pdb_file=args.pdb_file,
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/main.py", line 215, in run_peleffy
topology = Topology(molecule, parameters)
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/topology/topology.py", line 71, in init
self._build()
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/topology/topology.py", line 88, in _build
or len(list(self.parameters.atom_iterator)) == 0):
File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/forcefield/parameters.py", line 333, in atom_iterator
assert len(self['atom_names']) == len(self['atom_types'])
AssertionError: Size of atom parameter lists should match
I upload the FAD in format txt, but you should be able to change it back to pdb easily by rename it.
FAD.txt
This the job file I used
NDP.txt
As a temporary solution, I attach the templates that whould be generated with this PDB file,
templates.zip
This issue might be solved now with bugfix from PR #159.