HIPPOS-genref Configuration Options

There are two kinds of options, essential and optional. When nothing declared it means the option is essential. Some options have default value. Also keep in mind that all file names must never use space! So use underscore instead.

You can also inserting comments at the beginning of the line or after the option-value pair by inserting the # sign before the comment. Everything inserted after the # sign will be ignored by the software.

Input Options

  • residue_name

    value: list of residue_name , eg. ASP107 SER111 THR112

    The list of residue_name, each residue separated by space. It is used in PLANTS post-analysis but not in VINA analysis as pdbqt don’t hold the residue_name-residue_number pair field. However it is highly recommended to define it in VINA post analysis as it will be included in output file, making the results easier to interpret.

  • residue_number

    value: list of residue_number , eg. 80 84 85

    The list of residue number, each number separated by space. Essential option in VINA post-analysis but optional in PLANTS post-analysis.

  • proteins

    value: list of reference_protein, eg. protein1.mol2 protein2.mol2 protein3.mol2

    The list of reference_protein structure, each reference separated by space. Must be in mol2 or pdbqt format.

  • ligands

    value: list of reference_ligand , eg. ligand1.mol2 ligand2.mol2 ligand3.mol2

    The list of reference_ligand structure, each reference separated by space. Must be in mol2 or pdbqt format. Please note that the first reference_protein will be paired with first reference_ligand, the second reference_protein will be paired with second reference_ligand, and so on.

Output Options

  • outfile (optional)

    value: output_file_name, default genref-results.txt

Advanced Options

  • output_mode (optional)

    value: output_mode , default: full, options: full, full_nobb, and simplified

    output_mode define the bistring calculation and output. full means all interaction including the backbone interaction taken into account. full_nobb means backbone interactions are omitted. simplified means irrelevant interaction omitted (see Simplified Bitstring Rule). When this option not used output_mode full will be used.