Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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Start a New Project

You have to specify absolute paths for all files and directories. Unused fields should be blank. You need to specify at least one PDB file (although this will not be called "docking"...).

HADDOCK and project setup:
Current HADDOCK program directory:
Path of the new project:
Run number:
Number of molecules for docking (max. 6):
Define the various molecules for docking:
PDB file of 1st molecule:
PDB file of 2nd molecule:
PDB file of 3rd molecule:
PDB file of 4th molecule:
PDB file of 5th molecule:
PDB file of 6th molecule:
Segid of 1st molecule:
Segid of 2nd molecule:
Segid of 3rd molecule:
Segid of 4th molecule:
Segid of 5th molecule:
Segid of 6th molecule:
The next six entries are optional and only required to run HADDOCK from ensemble of structures. The list files should contain the full path and each filename (including path) should be between quotes.
file list for 1st molecule (opt.):
file list for 2nd molecule (opt.):
file list for 3rd molecule (opt.):
file list for 4th molecule (opt.):
file list for 5th molecule (opt.):
file list for 6th molecule (opt.):
Define the various restraint files:
AIR restraints:
distance restraints:
Dihedral angle restraints:
Hbonds restraints:
Residual dipolar couplings 1:
Residual dipolar couplings 2:
Residual dipolar couplings 3:
Residual dipolar couplings 4:
Residual dipolar couplings 5:
PCS restraints 1:
PCS restraints 2:
PCS restraints 3:
PCS restraints 4:
PCS restraints 5:
PCS restraints 6:
PCS restraints 7:
PCS restraints 8:
PCS restraints 9:
PCS restraints 10:
PCS tensor distance restraints file:
Diffusion anisotropy restraints 1:
Diffusion anisotropy restraints 2:
Diffusion anisotropy restraints 3:
Diffusion anisotropy restraints 4:
Diffusion anisotropy restraints 5:

Save the updated parameters somewhere in a directory as new.html
(use your browser save as menu if necessary).

Type haddock2.2 on the UNIX command line in the directory where you have saved your new.html file.