I try to use the HADDOCK web server. First I tested the E2A-HPR example, followed the steps, and downloaded the results. When I compared the result and identified crystal complex (1GGR), the top-rated pose cannot overlap well with 1GGR. So I downloaded the example result file from the website and did the comparison again, this time the two can overlap very well (see the attached pics). I’m wondering whether it’s a normal situation or I made some mistakes. Thank you!
Did you following the tutorial instructions step by step?
Yes, I followed step by step and the protein is prepared via PyMol. Thanks
Well - what can I say… Did you check other clusters?
Or try again
I’ve checked top five clusters, not found overlap one. I’d like to try again and will update my result. Thanks
Hello, I’ve checked other clusters first, and got overlap clusters (7 and 8), the 1-5 clusters have no good ovelap with 1GGR. Meanwhile, I submited another run and waiting for the result to see whether the top-rated cluster can overlap with 1GGR well. Thanks