ADL: ADL3 to ADL4 migration

Stéphane Téletchéa stephane.teletchea at jouy.inra.fr
Mon Oct 1 05:07:41 PDT 2007


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
#####################################################################

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901


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