Energy functions

1

Hi
I have a few questions

  1. can I please have a link to the the articles where the energy functions HADDOCK uses are written? vdv, desolvation, electrostatic, restraint etc.
  2. what OPLC model is used?
  3. when I use unambiguous restraint does it make a difference if I write 2.5 2.5 2 (so the distance is between 0.5-5) or if I write 3.5 1.5 1 (assuming the distance is between 2.5-5 anyways). does it make a difference in the calculations?
  4. what does the restraints violation mean if I only used unambiguous restrains? does that mean they were not followed or it in the upper/ lower limit?
    Thank you!
2

Also, can I run HADDOCK on my computer using multiple cores?
is the run on HADDOCK server faster then on a Linux super computer?

3

Also, can I run HADDOCK on my computer using multiple cores?

Yes you can - but it will take more manual steps. Check our online tutorial:

https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/

is the run on HADDOCK server faster then on a Linux super computer?

If you have plenty of resource running on your own cluster will be faster.But again the pre- and post-processing will require manual steps.

4

Thank you!
can you please answer the questions for the previous questions?
writing them again-

  1. can I please have a link to the the articles where the energy functions HADDOCK uses are written? vdv, desolvation, electrostatic, restraint etc.
  2. what OPLC model is used?
  3. when I use unambiguous restraint does it make a difference if I write 2.5 2.5 2 (so the distance is between 0.5-5) or if I write 3.5 1.5 1 (assuming the distance is between 2.5-5 anyways). does it make a difference in the calculations?
  4. what does the restraints violation mean if I only used unambiguous restrains? does that mean they were not followed or it in the upper/ lower limit?
    Thank you!