I have a protein (6eqe.pdb) which I have docked to a ligand using autodock vina. I want to model my query gene taking this receptor-ligand complex as the template. The ligand is identified as UNK in the pdb file. On modeling I am not getting all the atoms of the ligand in the modelled output (Only 1 carbon and 1 oxygen).Attached to this mail are the template file which has been docked to the ligand (6eqe_bhet.pdb) , the modelled protein with incomplete/erroneous ligand (ARN19002.1_Rhizobacter_gummiphilus_NS21.B99990001.pdb) and the alignment file for the same (ARN19002.1_Rhizobacter_gummiphilus_NS21.ali) .
Could you please look into the files?
Kindly let me know where I am going wrong.
Thanks and regards
Anwesha