HIPPOS 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.

Basic Options

  • docking_method

    value: vina or plants

  • docking_conf

    value: docking_configuration_file_name , eg. vina.conf or plants.conf

  • direct_ifp

    value: true or false, (default: false)

    If the value is set to true, it will use Direct IFP method and thus docking_method and docking_conf will be ignored.

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.

  • similarity_coef (optional)

    value: list of similarity_coef , eg. tanimoto or mcconnaughey or tanimoto mcconnaughey

    If the value is set then full_ref or full_nobb_ref or simplified_ref (depends on output_mode used) must be provided, so interaction fingerprint can be compared against reference.

    • full_ref

      value: bitstring1 bitstring2 ... n

      At least 1 uniform bitstring must be provided

    • full_nobb_ref

      value: bitstring1 bitstring2 ... n

      At least 1 uniform bitstring must be provided

    • simplified_ref

      value: bitstring1 bitstring2 ... n

      At least 1 simplified bitstring must be provided

  • protein

    value: protein file name , eg. protein.pdb

    The protein file name that will be used in Direct IFP mode. Format allowed: pdb, mol2, pdbqt.

  • ligand_files

    value: list of ligand name , eg. 3BO.pdb 3BR.pdb 3BS.pdb

    The list of ligand name that will be paired with the protein in Direct IFP mode.

  • ligand_list

    value: a file containing ligand file names , eg. ligand_list.txt

    The name of the file that contain ligand file names.

  • multiple_ligand_list

    value: list of file containing ligand file names , eg. ligand_list1.txt ligand_list2.txt ligand_list3.txt

    The list of file that contain ligand file names.

  • complex_list

    value: a filename containing list protein-ligand pair , eg. complex_list.txt

    In Direct IFP mode, if this value is set then protein, ligand_list, and multiple_ligand_list will not be required.

Output Options

  • full_outfile (optional)

    value: full_output_file_name , default: full_ifp.csv

    Only used by full output_mode. It is recommended to use the csv extensions for clarity.

  • full_nobb_outfile (optional)

    value: full_output_file_name , default: full_nobb_ifp.csv

    Only used by full_nobb output_mode. It is recommended to use the csv extensions for clarity.

  • simplified_outfile (optional)

    value: simplified_output_file_name , default: simplified_ifp.csv

    Only used by simplified output_mode. It is recommended to use the csv extensions for clarity.

  • sim_outfile (optional)

    value: similarity_output_file_name, default: similarity.csv

    Only used when the similarity coefficient is calculated.

  • logfile (optional)

    value: log_file_name , default: hippos.log

Advanced Options

  • output_mode (optional)

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

    The list of output_mode, at least one value required. When multiple value provided each value must be separated by space. Multiple value can only be used in HIPPOS without reference. When nothing provided output_mode full will be used.

  • docking_score (optional)

    value: yes or no , default: yes

    Extract the docking score of ligand poses from docking results and attach them to output file.

  • omit_interaction (optional)

    value: interaction_type and residue_name

    where interaction_type is one of the following value:

    • hydrophobic or HPB

    • aromatic or ARM

    • h_bond or HBD

    • electrostatic or ELE

    • h_bond_donor or HBD_DON

    • h_bond_acceptor or HBD_ACC

    • electrostatic_positive or ELE_POS

    • electrostatic_negative or ELE_NEG

    • aromatic_facetoface or ARM_F2F

    • aromatic_edgetoface or ARM_E2F

    While residue_name specify which residue will be omitted. Usage example:

    omit_interaction hydrophobic ARG223