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If one of your molecules is DNA/RNA, restraints are automatically created to preserve its structure. Uncheck this option if you are docking with unstructured DNA/RNA.

HADDOCK deletes by default all hydrogens except those bonded to a polar atom (N, O). Uncheck this option if you have NOEs or other specific restraints to non-polar hydrogens.

Random patches

Center of mass restraints



Surface contact restraints


Random exclusion


Radius of gyration restraint












Solvated docking mode

Cutoff for defining neighbouring flexible regions





In addition to distance restraints, you may specify dihedral and hydrogen bond restraints. These restraints can be inter- or intra-molecular.







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Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement



Energy constants per stage




Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement



Energy constants per stage




Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement



Energy constants per stage




Energy constants for dihedral angle restraints





Energy constants for radius-of-gyration restraints










SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage