Writing a `input.list` file

The input list is a flat text file with the paths of the targets;

# input.list
/home/rodrigo/projects/haddock-benchmark/data/complex1_r_u.pdb
/home/rodrigo/projects/haddock-benchmark/data/complex1_l_u.pdb
/home/rodrigo/projects/haddock-benchmark/data/complex1_ti.tbl
#
# comments are allowed, use it to organize your file
#
/home/rodrigo/projects/haddock-benchmark/data/complex2_r_u.pdb
/home/rodrigo/projects/haddock-benchmark/data/complex2_l_u.pdb
/home/rodrigo/projects/haddock-benchmark/data/complex2_ti.tbl
/home/rodrigo/projects/haddock-benchmark/data/complex2_ligand.top
/home/rodrigo/projects/haddock-benchmark/data/complex2_ligand.param

Note that this file must follow the pattern:

path/to/the/structure/NAME_receptor_suffix.pdb
path/to/the/structure/NAME_ligand_suffix.pdb

In the above example, complex1 and complex2 correspond thus to NAME, identifying the complex which is modelled. Each PDB file (indicated by the .pdb extension) has a suffix, this is extremely important as it will be used to organize the data. For example, the file complex1_r_u.pdb is the receptor of the target complex1 and complex1_l_u is the ligand of the same target.

In this example the suffixes are:

receptor_suffix: _r_u
ligand_suffix: _l_u

These suffixes are defined in the benchmark.yaml file, see here for more details.

The same logic applies to the restraints files, in the example above the pattern for the ambiguous restraint can be defined as ambig: "ti", so the file complex1_ti.tbl will be used as the ambiguous restraint for the target complex1, complex2_ti.tbl for the target complex2, etc. See section 3.2.2 for information specific to the definition of restraints when setting up a HADDOCK3.0 run.

HADDOCK supports many modified amino acids/bases/glycans/ions (check the full list). However if your target molecule is not present in this library, you can also provide it following the same logic; topology: "_ligand.top" and param: "_ligand.param" will use the files protein2_ligand.top and protein2_ligand.param for the target protein2.

IMPORTANT: For ensembles, provide each model individually and append a number to the suffix, for example: complex1_l_u_1.pdb, complex1_l_u_2.pdb, etc.

See below a full example of the input.list file

# -------------------------------- #
# 1A2K
./example/1A2K/1A2K_r_u.pdb
./example/1A2K/1A2K_l_u.pdb
./example/1A2K/1A2K_ligand.top
./example/1A2K/1A2K_ligand.param
./example/1A2K/1A2K_ti.tbl
./example/1A2K/1A2K_unambig.tbl
# 1GGR
./example/1GGR/1GGR_r_u.pdb
./example/1GGR/1GGR_l_u_1.pdb
./example/1GGR/1GGR_l_u_2.pdb
./example/1GGR/1GGR_l_u_3.pdb
./example/1GGR/1GGR_l_u_4.pdb
./example/1GGR/1GGR_l_u_5.pdb
./example/1GGR/1GGR_ti.tbl
# 1PPE
./example/1PPE/1PPE_l_u.pdb
./example/1PPE/1PPE_r_u.pdb
./example/1PPE/1PPE_ti.tbl
./example/1PPE/1PPE_hb.tbl
./example/1PPE/1PPE_unambig.tbl
# 2OOB
./example/2OOB/2OOB_l_u.pdb
./example/2OOB/2OOB_r_u.pdb
./example/2OOB/2OOB_ti.tbl
./example/2OOB/2OOB_hb.tbl
# -------------------------------- #

haddock-runner

Writing a input.list file

Writing a `input.list` file