Testset,Process,Complex/Ligand/Receptor,Problem
PDBBind_strucutres,ligand_preprocessing,6q4q_ligand,Can't kekulize mol.  Unkekulized atoms: 60 61 62 63 64 65 66 67 68
PDBBind_strucutres,p2rank,6d07_protein_processed, p2rank,no pocket detected
PDBBind_strucutres,diffdock,6o0h_ligand,HAPPENING | The test dataset did not contain 6o0h_ligand for 6o0h_ligand_preped.sdf and 6o0h_protein_processed_Hs.pdb.
PDBBind_strucutres,gnina_sdf,6hzd_ligand_pocket1,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
PDBBind_strucutres,gnina_sdf,6od6_ligand_pocket3,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
PDBBind_strucutres,gnina_sdf,6q36_ligand_pocket7,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
PDBBind_strucutres,gnina_sdf,6q38_ligand_pocket3,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
PDBBind_strucutres,vina,6rtn_ligand (all pockets),PDBQT parsing error: Atom type B is not a valid AutoDock type (atom types are case-sensitive). > ATOM     21  B   UNL     1      -3.994   1.927  -0.815  1.00  0.00     0.547 B
PDBBind_strucutres,vina,6uhu_ligand (all pockets),PDBQT parsing error: Atom type B is not a valid AutoDock type (atom types are case-sensitive). > ATOM     16  B   UNL     1      -3.769  -0.559   0.796  1.00  0.00     0.872 B
PDBBind_alphafold,p2rank,6qlt,no pocket detected
PDBBind_alphafold,p2rank,6d07,no pocket detected
PDBBind_alphafold,p2rank,6d08,no pocket detected
PDBBind_alphafold,diffdock,6o0h_AF,LM embeddings for complex 6o0h_AF did not have the right length for the protein.
PDBBind_alphafold,diffdock,6jib_AF,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
PDBBind_alphafold,diffdock,6olx_AF,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
PDBBind_alphafold,diffdock,6jid_AF,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
PDBBind_alphafold,gnina_sdf,6hlb_AF_pocket2,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
PDBBind_alphafold,gnina_sdf,6o5u_AF_pocket2,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
PDBBind_alphafold,tankbind,6n0m_AF,Aborted (core dumped),OMP: Error #15: Initializing libomp.so, but found unknown library already initialized.
PDBBind_alphafold,tankbind,6n96_AF,Aborted (core dumped),OMP: Error #15: Initializing libomp.so, but found unknown library already initialized.
PDBBind_alphafold,vina,6uhu_AF (all pockets),PDBQT parsing error: Atom type B is not a valid AutoDock type (atom types are case-sensitive). > ATOM     16  B   UNL     1      -3.769  -0.559   0.796  1.00  0.00     0.872 B
HQR_structures,ligand_preprocessing,6M2F__F0L_201,Explicit valence for atom # 38 N, 4, is greater than permitted
HQR_structures,ligand_preprocessing,6ML9__ARG_301,Explicit valence for atom # 0 N
HQR_structures,ligand_preprocessing,7K5N__PRO_301,Explicit valence for atom # 0 N, 4, is greater than permitted
HQR_structures,p2rank,5qsg,no pocket detected
HQR_structures,p2rank,6cqc,no pocket detected
HQR_structures,p2rank,6ky4,no pocket detected
HQR_structures,p2rank,6ha4,no pocket detected
HQR_structures,p2rank,6n5x,no pocket detected
HQR_structures,p2rank,6wnm,no pocket detected
HQR_structures,p2rank,6x39,no pocket detected
HQR_structures,p2rank,7ucd,no pocket detected
HQR_structures,p2rank,8az8,no pocket detected
HQR_structures,calculate_boxSize,7BAY__T7K_1411,Bad Conformer Id
HQR_structures,vina_prepare_ligand,6WNM__U5J_101,Molecule not OK, refusing to write PDBQT. LOG: atom number 19 has None type, mol name:
HQR_structures,vina_prepare_ligand,7BAY__T7K_1411,Molecule not OK, refusing to write PDBQT. LOG: atom number 23 has None type, mol name:
HQR_structures,diffdock,7BAY__T7K_1411,Bad Conformer Id
HQR_structures,diffdock,6MFY__PNS_1801,LM embeddings for complex 6MFY__PNS_1801 did not have the right length for the protein.
HQR_structures,gnina,7Z6W__IG7_201_pocketProteinCenter,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'
HQR_structures,smina,5ZM5__CLR_1001 (all pockets),Parse error on line 253 in file "5zm5_Hs.pdb": ATOM syntax incorrect: "As" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ATOM    250 AS   UNK A  24      37.780 -58.716 -30.139  0.00  0.00    +0.000 As
HQR_structures,vina,5ZM5__CLR_1001 (all pockets),PDBQT parsing error: Atom type As is not a valid AutoDock type (atom types are case-sensitive). > HETATM  250 AS   CAS A  24      37.780 -58.716 -30.139  1.00 68.45     0.000 As
HQR_alphafold,ligand_preprocessing,6ML9_AF__ARG_301,Explicit valence for atom # 0 N
HQR_alphafold,p2rank,6cqc,no pocket detected
HQR_alphafold,p2rank,6he6,no pocket detected
HQR_alphafold,p2rank,6p9e,no pocket detected
HQR_alphafold,p2rank,6x39,no pocket detected
HQR_alphafold,p2rank,7wrp,no pocket detected
HQR_alphafold,p2rank,8az8,no pocket detected
HQR_alphafold,calculate_boxSize,7BAY_AF__T7K_1411,Bad Conformer Id
HQR_alphafold,vina_prepare_ligand,7BAY_AF__T7K_1411,Molecule not OK, refusing to write PDBQT. LOG: atom number 23 has None type, mol name:
HQR_alphafold,diffdock,7BAY_AF__T7K_1411,Bad Conformer Id
HQR_alphafold,diffdock,5OY5_AF__BLA_600,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
HQR_alphafold,diffdock,6TNM_AF__ATP_802,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
HQR_alphafold,diffdock,6UEX_AF__Q5S_401,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
HQR_alphafold,diffdock,7OZ8_AF__NGS_601,linalg.svd: The algorithm failed to converge because the input matrix contained non-finite values.
HQR_alphafold,gnina,7Z6W_AF__IG7_201_pocketProteinCenter,Aborted (core dumped). terminate called after throwing an instance of 'numerical_error'