docking-protein-glycan-ilrmsd-test.cfg

# ==================================================
#      Protein-glycan docking with HADDOCK3
#
#  This example workflow will dock an unbound ligand
#  (generated with GLYCAM) to an unbound protein.
#
#  The IL-RMSD clustering is used here to cluster
#  complex structures
# ==================================================
clean=false
mode = "local"
ncores = 10
run_dir = "run1-ilrmsd-test"
# list, insert full path
molecules = [
    "data/1LMQ_r_u.pdb",
    "data/1LMQ_l_u.pdb",
    ] 

[topoaa] 

[rigidbody]
ambig_fname = "data/ambig.tbl"
sampling = 20
w_vdw = 1 

[caprieval]
reference_fname = "data/target.pdb" 

# rigidbody models containing glycans can be very similar to each other
# especially when the glycans are short and linear. ilRMSD clustering after
# rigidbody is useful to remove redundant models
[ilrmsdmatrix]

[clustrmsd]
criterion = 'maxclust'
n_clusters = 4 # the number of clusters to be formed

[seletopclusts]
top_models = 5 

[caprieval]
reference_fname = "data/target.pdb" 

[flexref]
ambig_fname = "data/ambig.tbl"
tolerance = 5 

[caprieval]
reference_fname = "data/target.pdb" 

[ilrmsdmatrix]

[clustrmsd]
criterion = 'distance'
linkage = 'average'
# test example, we pick every cluster
min_population = 1 
clust_cutoff = 2.5 

[caprieval]
reference_fname = "data/target.pdb" 

# Running final caprieval with allatoms parameter set to true to also
#  include the evaluation of protein side chains
#  in both the alignment process and irmsd, ilrmsd computations
# NOTE that all glycans atoms are always considered even without this option.
[caprieval]
allatoms = true
reference_fname = "data/target.pdb"

# ==================================================