ADL: ADL3 to ADL4 migration

Yang Ye leafyoung at yahoo.com
Mon Oct 1 07:26:00 PDT 2007


I don't use prodrg to draw molecular topology. My recommended workflow 
is Ghemical(or other commercial package), which are established modeling 
tool. In your case, it could be solved if you use openbabel to repair 
your file (by setting input and output both to PDB).

Regards,
Yang Ye

On 10/1/2007 8:07 PM, Stéphane Téletchéa wrote:
> Dear all,
>
> I have created more then 100 ligands using proDRG and this tool outputs 
> a pdbqt3 format for ligands. Since i'm willing to use autodock4 (for 
> instance to benefit from the better ernergy calculation but also from 
> the protein side-chain flexibility), it there an *automated* way to 
> convert the pdbqt 3 format into the v4 format ?
>
> My concern is about the error message i'm getting for some ligands:
> "autogrid4: WARNING:  Oxygen atom found with no bonded atoms, atom 
> serial number 1602, atom_type 6"
>
> This leads to wrong or no docking positions.
>
> For the moment i'm converting from the pdb file to the pbdqt format 
> using MGLtools :
> python2.4 $UTILITIES/prepare_ligand4.py -l ${ligand}.pdb -o 
> ${ligand}_a4.pdbqt -U nphs
>
> Anything i'm doing wrong?
>
> Thanks a lot in advance,
>
> Stéphane
>
> Starting PDB :
> #####################################################################
> HETATM    1  OAB DRG     1       1.160   1.570  -0.300  1.00 20.00 
>         O
> HETATM    2  CAE DRG     1       1.860   2.580  -0.090  1.00 20.00 
>         C
> HETATM    3  OAC DRG     1       2.970   2.590   0.490  1.00 20.00 
>         O
> HETATM    4  CAD DRG     1       1.320   3.920  -0.580  1.00 20.00 
>         C
> HETATM    5  CAA DRG     1       0.480   4.560   0.530  1.00 20.00 
>         C
> CONECT    1    2
> CONECT    2    1    3    4
> CONECT    3    2
> CONECT    4    2    5
> CONECT    5    4
> END
> #####################################################################
>
> Translated pdbqt4 file :
> #####################################################################
> REMARK  1 active torsions:
> REMARK  status: ('A' for Active; 'I' for Inactive)
> REMARK    1  A    between atoms: CAE_2  and  CAD_4
> ROOT
> HETATM    1  OAB DRG     1       1.160   1.570  -0.300  1.00 20.00 
> -0.647 OA
> HETATM    2  CAE DRG     1       1.860   2.580  -0.090  1.00 20.00 
> 0.185 C
> HETATM    3  OAC DRG     1       2.970   2.590   0.490  1.00 20.00 
> -0.647 OA
> ENDROOT
> BRANCH   2   4
> HETATM    4  CAD DRG     1       1.320   3.920  -0.580  1.00 20.00 
> 0.098 C
> HETATM    5  CAA DRG     1       0.480   4.560   0.530  1.00 20.00 
> 0.012 C
> ENDBRANCH   2   4
> TORSDOF 1
> #####################################################################
>
>   



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