ADL: Docking of gold complexes with flexible residues and ligand torsions

Gana Natarajan gantapa at gmail.com
Wed Mar 23 02:15:26 PDT 2016


Hi All,

I am trying to dock two large complexes of gold Au25(PET)18 and Au25(DMBT)18 which are gold clusters protected by ligands. The ligands are dimethylbenzenethiol (S-Ph-(CH3)2)and phenyl ethanethiol (S-CH2-CH2-Ph). There are eighteen of these ligands bonded to the surface of each gold cluster via the sulfur atom. Each molecule which has 25 gold atoms in its cluster core. In this case the ligand is Au25(PET)18 and the receptor is Au25(DMBT)18 are similar molecules but have different ligands. 

I have currently two problems: 

(i) I would like to make the S-C, C-C, C-C bonds in the PET ligand torsions active (but there are too many torsions 3*18=54 > 32). Is there any thing I could do about this other than selecting fewer rotatable bonds. 

(ii) I would like to use the flexible residues function to treat the DMBT  (S-Ph-(CH3)2) ligands as residues however, when I choose a residue name such as LIG1, LIG2, etc and select these residues in ADT and try to choose torsions it says the "Current Residues have no active torsions”. On the other hand, If I select all the atoms it highlights only a few Au-Au bonds as torsion-active.

How should I go about this to enable me to at least select the S-C bonds of the ligands to be rotatable, so that the benzene ring can rotate (but not the gold atoms). 

The script prepare_flexreceptor4.py also reports an error:
Traceback (most recent call last):
  File "./prepare_flexreceptor4.py", line 185, in <module>
    non_rotatable_bonds=all_bnds)
  File "/Library/MGLTools/1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 2673, in __init__
    flex_residues = self.flex_residues = self.process_residues(residues)
  File "/Library/MGLTools/1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 3035, in process_residues
    ntors = self.setAutoFlexFields(res)
  File "/Library/MGLTools/1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 3089, in setAutoFlexFields
    res.root = ca_atom[0]
  File "/Library/MGLTools/1.5.6/lib/python2.5/UserList.py", line 28, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range


I have attached the PDBQT files of the receptor Ag25(DMBT)18.

Any advice would be much appreciated, as would a speedy reply. 

Best Regards, 
Gana 




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