Alexandre Bonvin bio photo

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

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Project Setup

  • Edit your run.cns file
      For editing your run.cns file enter the absolute path of your run.cns file (e.g. /software/haddock/example/e2a-hpr/run1/run.cns):

    (Note: if the file does not display try using Firefox)

    Type haddock2.2 on the UNIX command line in the directory where you have saved your run.cns.

    HADDOCK also offers support for DNA. If one of the molecules is DNA and defined as DNA in run.cns HADDOCK expects to find a file called dna-rna_restraints.def in the data/sequence directory. This file allows you to define standard A-, B- or custom restraints for DNA such as base-pairing, puckering and backbone dihedral angles. You can edit using the same mechanism as for run.cns (see above) a template file that can be found in the protocols directory. Save the file as dna-rna_restraint.def into the data/sequence directory.

    Note: This dna-rna_restraint.def is automatically generated when using our 3D-DART web server to create and manipulate DNA models.