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Re: [modeller_usage] reg: modeling against docked protein-ligand complex



Hello Sir,
Could you tell me where am going wrong?

On Wed, Jul 15, 2020, 2:10 PM Anwesha Mohapatra <">> wrote:

Hello Sir,

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