Writing an 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_uligand_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 ambiguous restraints can be specified in the benchmark.yaml file 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 the relevant section 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
# -------------------------------- #