ADL: Help in covalent docking

Tushar Ranjan Moharana tusharranjan at
Mon Feb 10 22:51:45 PST 2014

I want to do covalent docking. As per the paper covalently linking ligand to side chain of amino acid and treating them as flexible residue gives excellent result. But when I did that ADT shows no root atom detected also it recognize ligand as a separate chain. I link ligand and protein side chain with pymol and generated ligand using online smile translater (this create pdb file based on drawing structure). Please suggest me something to solve the problem. 

Thanks a lot 

Tushar Ranjan Moharana 
B. Tech, NIT Warangal 
Ph. D student, CCMB 

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