ADL: Too many torsions

Jack Shultz jshultz at hydrogenathome.org
Wed Jun 3 17:39:20 PDT 2009


What ways to I have available to reduce the number of torsions? Can
this be achieved by reducing the number of flexible residues?

prepare_ligand4.py -l ligand.mol2 -o ligand.pdbqt

prepare_receptor4.py -U nphs_lps_waters -r receptor.pdb -o receptor.pdbqt

prepare_flexrecepotr4.py -l ligand.pdbqt -r receptor.pdbqt -g
receptor_rigid.pdbqt -x receptor_flex.pdbqt -s
receptor:A:TYR48_PHE86_ILE95_LEU97_TYR100_LEU104_GLN141_MET149_receptor:B:LYS102_GLN141_ASN143_ASP145_THR146_LEU147

prepare_gpf4.py  -l ligand.pdbqt -r receptor_rigid.pdbqt -p
custom_parameter_file=1 -p parameter_file=AD4_parameters.dat -p
ligand_types="A C HD N NA OA SA"

prepare_dpf4.py -l ligand.pdbqt -r receptor_rigid.pdbqt -p
compute_unbound_extended_flag=0 -p ga_run=10 -p
flexres=receptor_flex.pdbqt

autogrid4.exe  -p receptor_rigid.gpf -l out.glg

autodock4.exe  -p ligand_receptor_rigid.dpf -l out.dlg

autodock4: ERROR: PDBQT ERROR: too many torsions, maximum number of torsions is
32
autodock4: Aborting...

autodock4: Unsuccessful Completion.

On Mon, Jun 1, 2009 at 8:58 PM, Jack Shultz <jshultz at hydrogenathome.org> wrote:
> I had the same result with the recent download of MGLTools and Autodock4
>
> C:\Users\jshultz\test>prepare_ligand4.py -l ligand.mol2 -o ligand.pdbqt
>
> C:\Users\jshultz\test>prepare_receptor4.py -U nphs_lps_waters -r receptor.pdb -o
>  receptor.pdbqt
> adding gasteiger charges to peptide
>
> C:\Users\jshultz\test>prepare_flexdocking4.py -l ligand.pdbqt -r receptor.pdbqt
> -g receptor_rigid.pdbqt -x receptor_flex.pdbqt -s receptor:A:TYR48_PHE86_ILE95_L
> EU97_TYR100_LEU104_GLN141_MET149_receptor:B:LYS102_GLN141_ASN143_ASP145_THR146_L
> EU147
>
> C:\Users\jshultz\test>prepare_gpf4.py  -l ligand.pdbqt -r receptor_rigid.pdbqt -
> p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat -p ligand_types="
> A C HD N NA OA SA"
> setting ligand_types: newvalue= A C HD N NA OA SA
>
> C:\Users\jshultz\test>prepare_dpf4.py -l ligand.pdbqt -r receptor_rigid.pdbqt -p
>  compute_unbound_extended_flag=0 -p ga_run=10 -p flexres=receptor_flex.pdbqt
>
> C:\Users\jshultz\test>autogrid4.exe  -p receptor_rigid.gpf -l out.glg
>
> autogrid4: Successful Completion.
>
> C:\Users\jshultz\test>autodock4.exe  -p ligand_receptor_rigid.dpf -l out.dlg
> autodock4: ERROR:  All ATOM and HETATM records must be given before any nested B
> RANCHes; see line 194 in PDBQT file "ligand.pdbqt".
> - Show quoted text -
>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org



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