--chain flag error when dealing with pdb containing only the ligand

[Ignasi Puch Giner]

I was trying to use peleffy to obtain the parametrization with the OpenFF of the ligand I was dealing with by using the following text in a run script

#!/bin/bash
#SBATCH -J 6CSP_temp
#SBATCH --output=peleffy.out
#SBATCH --error=peleffy.err
#SBATCH --ntasks=48
#SBATCH --qos=debug
#SBATCH --time=00-01:00:00

module purge
export PELE_EXEC=/gpfs/projects/bsc72/PELE++/mniv/V1.7.1/bin/PELE-1.7.1_mpi
export SCHRODINGER=/gpfs/projects/bsc72/SCHRODINGER_ACADEMIC
export PATH=/gpfs/projects/bsc72/conda_envs/platform/1.6.0/bin:$PATH
export PELE_DATA=/gpfs/projects/bsc72/PELE++/mniv/V1.7.1/Data
export PELE_DOCUMENTS=/gpfs/projects/bsc72/PELE++/mniv/V1.7.1/Documents
export PELE_LICENSE=/gpfs/projects/bsc72/PELE++/license

module load intel mkl impi gcc
module load impi
module load boost/1.64.0

python -m peleffy.main 6CSP_lig_1.pdb -f 'openff_unconstrained-1.2.0.offxml' --with_solvent --chain L

where 6CSP_lig_1.pdb was the pdb file of the ligand and the following text was printed in the .err file.

------------------------------------------------------------
Open Force Field parameterizer for PELE 1.3.3
------------------------------------------------------------
 - General:
   - Input PDB: 6CSP_lig_1.pdb
   - Output path: None
   - Write solvent parameters: True
   - DataLocal-like output: False
 - Parameterization:
   - Force field: openff_unconstrained-1.2.0.offxml
   - Charge method: am1bcc
 - Rotamer library:
   - Resolution: 30
   - Exclude terminal rotamers: True
------------------------------------------------------------
 - Initializing molecule from PDB
   - Loading molecule from RDKit
   - Assigning stereochemistry from 3D coordinates
   - Setting molecule tag to 'LIG'
   - Representing molecule with the Open Force Field Toolkit
 - Generating rotamer library
   - Core set to the center of the molecule
 - Loading 'openff_unconstrained-1.2.0.offxml'
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 <module>
    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 203, in run_peleffy
    rotamer_library.to_file(output_handler.get_rotamer_library_path())
  File "/gpfs/projects/bsc72/conda_envs/platform/1.6.0/lib/python3.8/site-packages/peleffy/utils/output.py", line 149, in get_rotamer_library_path
    file_name = self._molecule.tag.upper().strip() + '.rot.assign'
AttributeError: 'list' object has no attribute 'tag'