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durrantlab / binana

BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study. We have also created a BINANA web-browser application.
http://durrantlab.com/binana-download/
Apache License 2.0
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ZeroDivisionError: float division by zero error + no atom named "X" warnings. #2

Open MarioAsti8 opened 8 months ago

MarioAsti8 commented 8 months ago

I'm getting the following error when running binana from a Python script with a set of proteins and ligands in .pdb format (extracted directly from the PDB). It starts fine but fails when getting to a certain complex:

Traceback (most recent call last): File "interactions_.py", line 60, in ligand, receptor = binana.load_ligand_receptor.from_files(lig_path, prot_path) File "binana-2.1/python\binana\load_ligand_receptor__init__.py", line 103, in from_files receptor.load_pdb_file(receptor_filename) File "binana-2.1/python\binana_structure\mol.py", line 243, in load_pdb_file self.load_pdb_from_text( File "binana-2.1/python\binana_structure\mol.py", line 204, in load_pdb_from_text self.assign_charges() File "binana-2.1/python\binana_structure\mol.py", line 953, in assign_charges self.charges_amines(atom_index, atom) File "binana-2.1/python\binana_structure\mol.py", line 842, in charges_amines elif num_neighors == 1 or atom.has_sp3_geometry(self): File "binana-2.1/python\binana_structure\atom.py", line 327, in has_sp3_geometry angles.append(angle_between_three_points(ncrs[0], ccr, ncrs[2]) * to_deg) File "binana-2.1/python\binana_utils_math_functions.py", line 146, in angle_between_three_points return angle_between_points(vector1, vector2) File "binana-2.1/python\binana_utils_math_functions.py", line 151, in angle_between_points new_point2 = return_normalized_vector(point2) File "C:\Users/Mario Astigarraga/binana-2.1/python\binana_utils_math_functions.py", line 160, in return_normalized_vector return Point(vector.x / dist, vector.y / dist, vector.z / dist) ZeroDivisionError: float division by zero

I am also getting mutliple warning messages like the following one:

WARNING: There is no atom named "NZ" in the protein residue LYS_89_A. Please use standard naming conventions for all protein residues to improve BINANA accuracy.

The residues mentioned indeed do not have the atom names stated when looking at the pdb file, but they appear in other residues. What issues may this cause? Thanks!

MarioAsti8 commented 8 months ago

The complex where the error happens is pdb 1H07, when calculating interactions between ligand ACE and the protein. The .pdb file was retrieved from the PDB (Biological Assembly 1 in .pdb). Ligand coordinates where removed from the file and pasted into a new ligand file, also .pdb.