The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab
Hi, I recently run a protein ligand docking in haddock 2.4 webserver. The result gave me a positive desolvation energy. Is it something to worry about? Like should I change something in the parameters while running the docking. I am trying to reproduce a published result and they have reported a negative desolvation energy. I am uploading the screenshot of result for reference.
Thank you for your reply. I am new to docking…could you please tell me what all parameters among the above given by haddock should I focus on to say that this ligand has docked well to the protein?
The only way for you to know if the ‘ligand has docked well’, is to compare it with a reference structure, and compute the ligand-RMSD.
If you obtain the same conformation (ligand-RMSD as small as possible), you can say you managed to reproduce the result of that particular paper.
Also, note that reported values here are per-cluster (1.8 +/- 0.5 in that case).
If you download the corresponding structures, you can investigate the actual scores in the PDB file for each complex, and maybe one of them contains a negative desolvation energy.
