ADL: Too many torsions

Stefano Forli forli at scripps.edu
Wed Jun 3 18:22:08 PDT 2009


Hi Jack,

the number of residues you want to treat as flexible is definitely too big. If you need to 
sample the conformation of 14 residues, probably it's better to orient your calculations 
toward a molecular dynamics simulation instead of docking.

As a limited alternative, you could prepare your flexible receptor by choosing the flex 
residues inside ADT, disable some of their torsions and saving them a pdbqt file, but this 
is still an extreme docking calculation.


Stefano




Jack Shultz wrote:
> 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 -
>>
> 
> 
> 


-- 
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-5
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at scripps.edu


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