Given `WARNING: Flexible residue outside box.` when centering off of reactive res

Input: mk_prepare_receptor.py --pdb receptor_reduced.pdb -o receptor.pdbqt -r "A:SER:103" --box_center_off_reactive_res --box_size 32 32 32
Gridbox and receptor_reduced.pdb sent on Slack.
Full output:

/gpfs/home/ahansel/micromamba/envs/cryokit/bin/mk_prepare_receptor.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html

  __import__('pkg_resources').require('meeko==0.6.0a3')

Flexible residues:
chain resname resnum is_reactive reactive_atom
    A     SER    103        True            OG

reactive_flexres={('A', 'SER', 103): 'OG'}

{'mutate_res_dict': {'A:GLU:2': 'A:GLU:2', 'A:GLU:5': 'A:GLU:5', 'A:HIS:14': 'A:HIE:14', 'A:ASP:33': 'A:ASP:33', 'A:GLU:40': 'A:GLU:40', 'A:ASP:44': 'A:ASP:44', 'A:HIS:45': 'A:HIE:45', 'A:ASP:52': 'A:ASP:52', 'A:ASP:55': 'A:ASP:55', 'A:GLU:58': 'A:GLU:58', 'A:GLU:60': 'A:GLU:60', 'A:GLU:63': 'A:GLU:63', 'A:ASP:67': 'A:ASP:67', 'A:ASP:73': 'A:ASP:73', 'A:ASP:75': 'A:ASP:75', 'A:ASP:81': 'A:ASP:81', 'A:ASP:84': 'A:ASP:84', 'A:GLU:87': 'A:GLU:87', 'A:ASP:94': 'A:ASP:94', 'A:GLU:95': 'A:GLU:95', 'A:HIS:111': 'A:HID:111', 'A:ASP:115': 'A:ASP:115', 'A:GLU:118': 'A:GLU:118', 'A:HIS:126': 'A:HIE:126', 'A:GLU:127': 'A:GLU:127', 'A:ASP:136': 'A:ASP:136', 'A:ASP:142': 'A:ASP:142', 'A:ASP:145': 'A:ASP:145', 'A:ASP:146': 'A:ASP:146', 'A:HIS:149': 'A:HIE:149', 'A:GLU:154': 'A:GLU:154', 'A:GLU:157': 'A:GLU:157', 'A:GLU:165': 'A:GLU:165', 'A:ASP:173': 'A:ASP:173', 'A:ASP:182': 'A:ASP:182', 'A:GLU:184': 'A:GLU:184', 'A:GLU:185': 'A:GLU:185', 'A:GLU:189': 'A:GLU:189', 'A:GLU:199': 'A:GLU:199', 'A:GLU:201': 'A:GLU:201', 'A:HIS:207': 'A:HID:207', 'A:ASP:213': 'A:ASP:213', 'A:ASP:214': 'A:ASP:214', 'A:ASP:220': 'A:ASP:220', 'A:ASP:229': 'A:ASP:229', 'A:ASP:237': 'A:ASP:237', 'A:GLU:245': 'A:GLU:245', 'A:ASP:252': 'A:ASP:252', 'A:HIS:257': 'A:HID:257', 'A:GLU:265': 'A:GLU:265', 'A:ASP:269': 'A:ASP:269', 'B:GLU:2': 'B:GLU:2', 'B:GLU:5': 'B:GLU:5', 'B:HIS:14': 'B:HIE:14', 'B:ASP:33': 'B:ASP:33', 'B:GLU:40': 'B:GLU:40', 'B:ASP:44': 'B:ASP:44', 'B:HIS:45': 'B:HIE:45', 'B:ASP:52': 'B:ASP:52', 'B:ASP:55': 'B:ASP:55', 'B:GLU:58': 'B:GLU:58', 'B:GLU:60': 'B:GLU:60', 'B:GLU:63': 'B:GLU:63', 'B:ASP:67': 'B:ASP:67', 'B:ASP:73': 'B:ASP:73', 'B:ASP:75': 'B:ASP:75', 'B:ASP:81': 'B:ASP:81', 'B:ASP:84': 'B:ASP:84', 'B:GLU:87': 'B:GLU:87', 'B:ASP:94': 'B:ASP:94', 'B:GLU:95': 'B:GLU:95', 'B:HIS:111': 'B:HID:111', 'B:ASP:115': 'B:ASP:115', 'B:GLU:118': 'B:GLU:118', 'B:HIS:126': 'B:HIE:126', 'B:GLU:127': 'B:GLU:127', 'B:ASP:136': 'B:ASP:136', 'B:ASP:142': 'B:ASP:142', 'B:ASP:145': 'B:ASP:145', 'B:ASP:146': 'B:ASP:146', 'B:HIS:149': 'B:HIE:149', 'B:GLU:154': 'B:GLU:154', 'B:GLU:157': 'B:GLU:157', 'B:GLU:165': 'B:GLU:165', 'B:ASP:173': 'B:ASP:173', 'B:ASP:182': 'B:ASP:182', 'B:GLU:184': 'B:GLU:184', 'B:GLU:185': 'B:GLU:185', 'B:GLU:189': 'B:GLU:189', 'B:GLU:199': 'B:GLU:199', 'B:GLU:201': 'B:GLU:201', 'B:HIS:207': 'B:HID:207', 'B:ASP:213': 'B:ASP:213', 'B:ASP:214': 'B:ASP:214', 'B:ASP:220': 'B:ASP:220', 'B:ASP:229': 'B:ASP:229', 'B:ASP:237': 'B:ASP:237', 'B:GLU:245': 'B:GLU:245', 'B:ASP:252': 'B:ASP:252', 'B:HIS:257': 'B:HID:257', 'B:GLU:265': 'B:GLU:265', 'B:ASP:269': 'B:ASP:269'}}

WARNING: Flexible residue outside box.

WARNING: Strongly recommended to use a box that encompasses flexible residues.

For reactive docking, pass the configuration file to AutoDock-GPU:
    autodock_gpu -C 1 --import_dpf receptor.reactive_config --flexres receptor_flex.pdbqt -L <ligand_filename>

Files written:
           receptor_flex.pdbqt <-- flexible receptor input file
          receptor_rigid.pdbqt <-- static (i.e., rigid) receptor input file
receptor_suggested-config.json <-- log of automated decisions for user inspection
    boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid)
            receptor_rigid.gpf <-- autogrid input file
        receptor_rigid.gpf.pdb <-- PDB file to visualize the grid box
        receptor_rigid.box.txt <-- Vina-style box dimension file
      receptor.reactive_config <-- reactive parameters for AutoDock-GPU
forlilab / Meeko

Given `WARNING: Flexible residue outside box.` when centering off of reactive res #85
