Am using autodock 4.2, after docking my compound structures looks different in complex (protein -ligand). I want to know why my compounds looks like this?
i have prepared ligand and checked the following methods.
- Downloaded from pubchem/kegg - directly given as input
- Downloaded from pubchem/kegg - Energy minimized then given as input
- Drawn structure - directly given as input
- Drawn structure - Energy minimized then given as input
Energy minimization(EM) was performed separately in two ways, (i) docking server (MMFF94 and Gasteiger charges at PH 7) and (ii) Charmm (DS 3).
each structures was given separately to perform docking.
While analysis the ligand structures looks different, ligand structures (few) attached along with this post.
Please give your valuable suggestions... Thanks in advance....!