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PostPosted: Wed Oct 21, 2009 4:09 am 
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Joined: Sat Aug 08, 2009 10:54 am
Posts: 8
Hello all
I am using autodock4 to dock an oligosaccharide in protein. I read in the manual that maximum number torsions allowed by autodock4 is 32. I want to be clear that is this number 32 is allowed only in flexible part of the protein ?? or sum of Active rotatble bonds in flexible part of the protein and torsions of ligand should be less that 32 ??
I have 16 active torsions in the ligand and 13 active torsions in flexible part of protein even then i am getting the error on .dlg file that
.
.
.
.
Found parameters for atom 85, atom type "A", grid map index = 0
Found parameters for atom 86, atom type "A", grid map index = 0
Found parameters for atom 87, atom type "C", grid map index = 1
/usr/local/bin/autodock4: ERROR: PDBQT ERROR: too many torsions, maximum number of torsions is 32
/usr/local/bin/autodock4: Aborting...

/usr/local/bin/autodock4: Unsuccessful Completion.

Please find the attached pdbqt files of ligand and protein (macromolecule_rsl_flex.pdbqt). I will be happy if someone could help me in understanding my mistake..
thanking u all


Attachments:
File comment: Docking parameter file
1_bgatsch.dpf [3.28 KiB]
Downloaded 221 times
File comment: macromolecule flex residue file e
macromol_rsl_flex.pdbqt [6.1 KiB]
Downloaded 211 times
File comment: ligand PDBQT file
ligand_1_bga_tsch.pdbqt [4.73 KiB]
Downloaded 209 times
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