Math domain error in docking prep (4bps)

jyaacoub commented 1 year ago

v_prep8 subprocess 10 failed to complete due to following error:

Processing 4bps     : 202 / 310     : 0 errors
setting PYTHONHOME environment
adding gasteiger charges to peptide
Traceback (most recent call last):
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7//MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py", line 204, in <module>
    dict=dictionary)    
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 558, in __init__
    version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 141, in __init__
    self.addCharges(mol, charges_to_add)
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 227, in addCharges
    chargeCalculator.addCharges(mol.allAtoms)
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/MolKit/chargeCalculator.py", line 80, in addCharges
    babel.assignHybridization(atoms)
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/PyBabel/atomTypes.py", line 136, in assignHybridization
    self.valence_three()
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/PyBabel/atomTypes.py", line 231, in valence_three
    angle3 = bond_angle(l.coords, a.coords, m.coords)
  File "/cluster/home/t122995uhn/lib/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/PyBabel/util.py", line 53, in bond_angle
    else: angle = (math.acos(cos_theta)) * RAD_TO_DEG
ValueError: math domain error
removed ‘/cluster/projects/kumargroup/jean/data/refined-set//4bps/4bps_protein_temp.pdb’
1 molecule converted
Error: One or more prep files not found for 4bps

jyaacoub commented 1 year ago

This means the proteins for the following PDB codes don't have prepared pdbqt files:

4bps
4bt3
4bt4
4bt5
4bup
4c1y
4cd4
4cd5
4cpy
4cpz
4cs9
4czs
4d1j
4del
4dhl
4dsy
6of5
4dmw
4dst
4elf
4elg
4elh

jyaacoub commented 1 year ago

This means the proteins for the following PDB codes don't have prepared pdbqt files:
4bps
4bt3
4bt4
4bt5
4bup
4c1y
4cd4
4cd5
4cpy
4cpz
4cs9
4czs
4d1j
4del
4dhl
4dsy
6of5
4dmw
4dst
4elf
4elg
4elh

4bps is the only issue here and so, skipping that for now. I have prepared the rest of the codes with no issues.

jyaacoub / MutDTA

Math domain error in docking prep (4bps) #3