Where to find lowest energy structure?

HADDOCK
1

Hello HADDOCK users!

I’m a newcomer and I’ve run some docking calculations using the lates HADDOCK web server. In the results page I see a line as “RMSD from the overall lowest-energy structure”.
Where can I find that structure?

Thanks,
Reza

2

If you download the full run archive, look into the structures/it1/water directory - it is the first PDB file listed in file.list

3

OK cool. I see complex_1w.pdb.
Just to be clear, how come this lowest energy structure is also the highest ranked structure in the first cluster on the results page?

4

A good sign then - it does not have to be so, but in your case the top ranked model also belongs to the top ranked cluster

5

I have a doubt about this, each pdb file has a “Binding Energy” line. But when comparing the values of the pdb files and those listed in file.list they are very different. Also, sometimes the lowest energy structure in file.list is not the same as those with the lowest “Link Energy” value in the pdb files. Which score value should I use, the one from the pdb file or the file.list?

6

file.list contains the HADDOCK score.

The binding energy is something different (old stuff we should remove)

7

It seems that SPDBV can calculate the lowest energy of a protein