after finished docking using autodock vina, when i was trying to extract the docked models to find out the best docked models,that time i noticed that only 8 files of docked models created, but it should be 9 files. so is there any lack of conformation in my ligand? how can i get 9 files of docked model?
I converted the sdf file of ligand to pdf by openbabel,then converted to pdbqt by autodock tools.i collected the sdf file of 3D conformer from pubchem.
During control docking,i did not face this problem.
Please help me out to solve this problem.
Thanks in advance
I'd suggest you to check the docking output file to see if 9 poses were indeed generated. While running a docking with ADVina, you can specify the max number of generated conformers, but it can give you fewer ones (depending on the energy range set, for instance).
"Why don't I get as many binding modes as I specify with "--num_modes"?
This option specifies the maximum number of binding modes to output. The docking algorithm may find fewer "interesting" binding modes internally. The number of binding modes in the output is also limited by the "energy_range", which you may want to increase.
Source: http://vina.scripps.edu/manual.html