Dear all, when I use HADDOCK for docking the interaction between a lipase and an inhibitor (small molecular), a problem emerged when I selected the active residues (144,168,231) of the protein (lipase). it showed :"None of the active residues are accessible”. What does this mean? How to solve it? help!
Genhong
Well it means that your active residues are not accessible (they are buried).
You can turn off this option if you have an expert/guru level.
I am having the same problem. One of the molecules I am docking (2is4), I have selected few residues from experimental data as active residues, and HADDOCK considered them as non-accessible. Never had this problem before. The protein also has some unstructured part, which all the residues are almost available and when I tried these residues, they were also shown as non-accessible. Any solutions would be so much appreciated 
Did you turn off the option to Remove buried active/passive residues from selection? There was a small issue with ligands, but that has been fixed.
We have indeed implemented the filtering out of non solvent accessible residues.
This was done because of some users defining large number of active residues (e.g. selecting the entire sequence), which is a VERY BAD idea leading to a pure waste of computational resources.
How would you expect buried residues to be able to make contacts?
PS: If you define your own restraints, e.g. using our GentTbl server you can bypass this. You will have then to upload the restraints as ambiguous ones during the submission process (does require expert level access).
https://alcazar.science.uu.nl/services/GenTBL/
But be wise in the way you define your restraints!
Remember you are using a free resource and avoid wasting precious CPU time
Thanks for all your kind answers. I managed to dock after removing buried active/passive residues from selection
On the other hand my question was more about the accessibility of the residues. As @amjjbonvin said, I do not expect the buried residues to make contact, but the active residues I selected are on the surface. In order to avoid that, I selected other residues in the vicitinity with much more exposed and longer side chains, and those were again non-accessible. Then I tried other regions of the same protein -unstructured region- and again that was considered as non-accessible.
Thanks again for all the suggestions !
On the other hand my question was more about the accessibility of the residues. As @amjjbonvin said, I do not expect the buried residues to make contact, but the active residues I selected are on the surface. In order to avoid that, I selected other residues in the vicitinity with much more exposed and longer side chains, and those were again non-accessible. Then I tried other regions of the same protein -unstructured region- and again that was considered as non-accessible.
This is strange. Our cutoff is 15% relative surface area.
Can you share your PDF file (via email) and indicate which residues you are selecting?
Sure I can. Which email address can I use?
I somehow, just found out that my mail was returned for reason. Anyhow, I solved this issue by using DisVis to determine which residues after the interaction analysis, and it worked totally fine. Also my PDB file had some problems in numbering of the residues after removing double occupancies.
Self-solved issue! The best ones