50.00% of output was not generated for this module and tolerance was set to 0.00%.

Yuanhang2024 commented 2 months ago

Describe the bug

[2024-05-04 22:03:31,746 libutil ERROR] 50.00% of output was not generated for this module and tolerance was set to 0.00%.

To Reproduce Running with Config below:

# ====================================================================
# Protein-ligand docking example

# directory in which the scoring will be done
run_dir = "Nb17-ID3239"

# execution mode
mode = "local"
ncores = 40
# in which queue the jobs should run, if nothing is defined
#  it will take the system's default
# queue = "short"
# concatenate models inside each job, concat = 5 each .job will produce 5 models
concat = 5
#  Limit the number of concurrent submissions to the queue
queue_limit = 100

# molecules to be docked
molecules =  [
    "data/6vxf_ABCG2.pdb",
    "data/CycPeptMPDB_ID_3239_ChainB.pdb"
    ]

# ====================================================================
[topoaa]
autohis = true
ligand_param_fname = "data/ligand-prodrg.param"
ligand_top_fname = "data/ligand-prodrg.top"
delenph = false

[rigidbody]
tolerance = 5
ambig_fname = "data/ambig-active-rigidbody.tbl"
ligand_param_fname = "data/ligand-prodrg.param"
ligand_top_fname = "data/ligand-prodrg.top"
sampling = 20
w_vdw = 1.0

[caprieval]

[seletop]
select = 200

[caprieval]

[flexref]
tolerance = 5
ambig_fname = "data/ambig-passive.tbl"
ligand_param_fname = "data/ligand-prodrg.param"
ligand_top_fname = "data/ligand-prodrg.top"
mdsteps_rigid = 0
mdsteps_cool1 = 0

[caprieval]

[rmsdmatrix]
resdic_A = [247,248,249,250,251,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,]
resdic_B = [ 1 ]

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

[seletopclusts]
top_models = 4

[caprieval]

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

Expected behavior A clear and concise description of what you expected to happen.

Configuration (optional - remove if not relevant)

OS:CentOS

Yuanhang2024 commented 2 months ago

The examples from the protein-ligand-docking folder can run normally.

amjjbonvin commented 2 months ago

It’s not a bug - most likely bad quality of your staring models - or a problem with the ligand param/topo files

These are required if you want to dock some other ligands and should be provided to haddock

Our haddock2.4 server generate those automatically. The standalone version does not

Yuanhang2024 commented 2 months ago

Thank you so much for answering, but I have 5000 samples to deal with, so I can't rely on the server. How can I generate the .top and .param files in large scales?

amjjbonvin commented 2 months ago

Some tips can be found at:

https://www.bonvinlab.org/software/haddock2.4/faq/#small-ligand-docking-with-haddock HADDOCK2.4 manual - Frequently Asked Questions bonvinlab.org

Further you could check the BioExcel BioBB modules. There is one to generate CNS topo/param file using acepype

Check: https://github.com/bioexcel/biobb_wf_ligand_parameterization (look for the CNS parametrisation tutorial)