ADL: Binding energy and flexible receptor

Michele Lunelli efunit at
Thu Mar 6 06:26:13 PST 2008

Finally I have found the mistake that I made: I left the flexible residues in 
the pdbqt used to calculate the grid. Therefore there is an "energy explosion" 
when the energy is evaluated during the docking, because of the bad clashes of 
the flexible residues with themselves.


Michele Lunelli wrote:
> Dear all,
> I performed a docking simulation with autodock4 of a small peptide and a 
> protein, obtaining reasonable results, with a binding energy of -4.5 kcal/mol. 
> However, there are two protein residues, a tyrosine and a phenilalanine, which I 
> think could obstacle the binding of the peptide. Therefore I set the sidechain 
> of these two residues as flexible. However, now the lowest binding energy 
> results 1160 kcal/mol, because the internal receptor energy is around 1170 
> kcal/mol! (the structure of the receptor has been taken from the PDB, determined 
> by NMR).
> What is the meaning of this very high binding energy? How can be compared with 
> the binding energy obtained with rigid receptor?
> Moreover, I noticed that the conformation of the two flexible residues is the 
> same for almost all the conformations found. I thought to some error in the 
> input file, but the pdbqt file of the flexible residues looks ok.
> Thank you advance for any suggestion,
> Michele Lunelli
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