Hello,
I’m quite new to HADDOCK and currently exploring the local version 2.4. I am interested in finding out if it is possible to score individual structures (for example, the crystal structure of an already bound form) without any refinement. I would like to compare this score to the scores obtained through the docking process to see how much improvement occurs. If this is possible, what is the easiest way to do it?
Thanks,
Enna
Dear Enna,
As a new user of HADDOCK, I would suggest to use haddock3 local version.
The configuration files are much easier to generate, and we have implemented dedicated analysis tools in it.
Also, it is very well suited for what you are trying to do, and we provide good scoring workflow examples.
If you want to stick to haddock 2.4, basically what is required is to reduce the number of steps during it1 and itw to 0.
Search for parameter names: cool1_steps, cool2_steps, cool3_steps, watercoolsteps, waterheatsteps, waterrefine, watersteps and initiosteps and set their value to 0 is the parameters.json file.
You could also try the webserver refinement protocols and select the Energy Minimization protocol.
I know you do not want to apply any refinement on the crystal structure, but it is always good to have a small energy minimization of structures using the same force field implemented in CNS, as the haddock scoring function was tuned based on this.
With the hope this helps you.
Cheers !
To add to Victor’s answer, two options:
Use the refinement server selecting only the energy minimisation protocol
Use HADDOCK3 with the emscoring module (see examples)
A short minimisation is recommended in all cases.