haddocking · amjjbonvin · Aug 10, 2026 · Aug 5, 2026 · Aug 5, 2026 · Aug 10, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,6 @@
 # Changelog
 
+- 2026-08-05: Harmonised running mode of test config files - Issue #1655
 - 2026-08-10: Added missing improper for HYP - Issue #1662
 - 2026-08-05: Removed identical duplicate `ANGLe` statements from `protein-allhdg5-4.param` and `protein-CG-Martini-2-2.param` - Issue #1589
 - 2026-08-04: Added workflow module ordering validation - related to Issue #1530

diff --git a/examples/analysis/alascan-complex-test.cfg b/examples/analysis/alascan-complex-test.cfg
@@ -9,7 +9,12 @@
 # ==================================================
 
 # General parameters
+
+# directory for the run
 run_dir = "run1-alanine-scan-complex"
+
+# execution mode
+mode = "local"
 ncores = 10
 
 # Input

diff --git a/examples/analysis/alascan-test.cfg b/examples/analysis/alascan-test.cfg
@@ -7,7 +7,12 @@
 # ==================================================
 
 # General parameters
+
+# directory for the run
 run_dir = "run1-alanine-scan"
+
+# execution mode
+mode = "local"
 ncores = 10
 
 # Input

diff --git a/examples/analysis/contmap-test.cfg b/examples/analysis/contmap-test.cfg
@@ -10,15 +10,16 @@
 # ================= #
 # Global parameters #
 # ================= #
-# directory in which the analysis will be performed
+
+# directory for the run
 run_dir = "test_contmap"
-# Number of CPU cores to use
-ncores = 5
+
+# execution mode
 mode = "local"
+ncores = 10
+
 # Input molecules
 molecules = ["../data/1a2k_r_u.pdb", "../data/1a2k_l_u.pdb"]
-# Disable post-processing
-postprocess = true
 
 # =================== #
 # Workflow definition #

diff --git a/examples/analysis/rnascan-test.cfg b/examples/analysis/rnascan-test.cfg
@@ -7,7 +7,12 @@
 # ==================================================
 
 # General parameters
+
+# directory for the run
 run_dir = "run1-rna-scan"
+
+# execution mode
+mode = "local"
 ncores = 10
 
 # Input

diff --git a/examples/analysis/topoaa-caprieval-test.cfg b/examples/analysis/topoaa-caprieval-test.cfg
@@ -1,7 +1,7 @@
 # ====================================================================
 # Capri analysis example
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-topoaa-caprieval-test"
 
 # compute mode

diff --git a/examples/analysis/topoaa-clustfcc-test.cfg b/examples/analysis/topoaa-clustfcc-test.cfg
@@ -4,7 +4,8 @@
 # ====================================================================
 # Define global parameters
 # ====================================================================
-# directory in which the scoring will be done
+
+# directory for the run
 run_dir = "run1-topoaa-clustfcc-test"
 
 # compute mode

diff --git a/examples/analysis/topoaa-ilrmsdmatrix-clustrmsd-test.cfg b/examples/analysis/topoaa-ilrmsdmatrix-clustrmsd-test.cfg
@@ -8,7 +8,8 @@
 # Finally, [caprieval] to evaluate the clustered models 
 #  based on CAPRI criterions.
 # ====================================================================
-# directory in which the scoring will be done
+
+# directory for the run
 run_dir = "run1-topoaa-ilrmsdmatrix-clustrmsd-test"
 
 # compute mode

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # Protein-protein docking example with NMR-derived ambiguous interaction restraints
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-CDR-NMR-CSP-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-clt-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # Protein-protein docking example with NMR-derived ambiguous interaction restraints
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-CDR-acc-cltsel-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-CDR-accessible-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # Protein-protein docking example with NMR-derived ambiguous interaction restraints
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-CDR-acc-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-ranairCDR-clt-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-ranairCDR-clt-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # Protein-protein docking example with NMR-derived ambiguous interaction restraints
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-ranairCDR-cltsel-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-antibody-antigen/docking-antibody-antigen-ranairCDR-test.cfg b/examples/docking-antibody-antigen/docking-antibody-antigen-ranairCDR-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # Protein-protein docking example with NMR-derived ambiguous interaction restraints
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-ranairCDR-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-multiple-ambig/docking-multiple-tbls-test.cfg b/examples/docking-multiple-ambig/docking-multiple-tbls-test.cfg
@@ -2,12 +2,12 @@
 # Protein-protein docking example with multiple arctic3d-derived 
 # ambiguous interaction restraints
 
-# directory in which the docking will be done
+# directory for the run
 run_dir = "run1-multiple-ambig-test"
 
 # compute mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-nanobody-antigen/docking-nanobody-antigen-CDR-loose-epi-test.cfg b/examples/docking-nanobody-antigen/docking-nanobody-antigen-CDR-loose-epi-test.cfg
@@ -3,12 +3,12 @@
 # with loose epitope definition
 # ====================================================================
 
-# directory in which the results will be stored
+# directory for the run
 run_dir = "run1-CDR-loose-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules = [

diff --git a/examples/docking-nanobody-antigen/docking-nanobody-antigen-CDR-mutagenesis-epi-test.cfg b/examples/docking-nanobody-antigen/docking-nanobody-antigen-CDR-mutagenesis-epi-test.cfg
@@ -3,12 +3,12 @@
 # with true paratope and epitope definition
 # ====================================================================
 
-# directory in which the results will be stored
+# directory for the run
 run_dir = "run1-CDR-mutagenesis-epi-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules = [

diff --git a/examples/docking-nanobody-antigen/docking-nanobody-antigen-Para-Epi-test.cfg b/examples/docking-nanobody-antigen/docking-nanobody-antigen-Para-Epi-test.cfg
@@ -3,12 +3,12 @@
 # with true paratope and epitope definition
 # ====================================================================
 
-# directory in which the results will be stored
+# directory for the run
 run_dir = "run1-Para-Epi-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules = [

diff --git a/examples/docking-nanobody-antigen/docking-nanobody-antigen-mix-loose-epi-test.cfg b/examples/docking-nanobody-antigen/docking-nanobody-antigen-mix-loose-epi-test.cfg
@@ -3,12 +3,12 @@
 # with loose epitope definition and mixed nanobody restraints
 # ====================================================================
 
-# directory in which the results will be stored
+# directory for the run
 run_dir = "run1-CDR-mix-loose-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules = [

diff --git a/examples/docking-nucleosome-PRC1/docking-nucleosome-PRC1-CG-test.cfg b/examples/docking-nucleosome-PRC1/docking-nucleosome-PRC1-CG-test.cfg
@@ -2,7 +2,7 @@
 # Protein-protein docking example with NMR-derived ambiguous interaction restraints
 # ====================================================================
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-CG-test"
 
 # execution mode
@@ -15,18 +15,19 @@ molecules =  [
     "data/3rpg_clean.pdb"
     ]
 
-postprocess = True 
-
 # ====================================================================
 # Parameters for each stage are defined below, prefer full paths
 # ====================================================================
 
 [topoaa]
+log_level = 'verbose'
 
 [topocg]
 cgffversion = "martini2"
+log_level = 'verbose'
 
 [rigidbody]
+log_level = 'verbose'
 ambig_fname = "data/ambig.tbl"
 unambig_fname = "data/unambig.tbl"
 randremoval = false
@@ -45,6 +46,7 @@ reference_fname = "data/4r8p_reference.pdb"
 fnat_cutoff = 7.0 # cutoff for coarse-grained structures
 
 [flexref]
+log_level = 'verbose'
 ambig_fname = "data/ambig.tbl"
 unambig_fname = "data/unambig.tbl"
 randremoval = false
@@ -55,8 +57,10 @@ reference_fname = "data/4r8p_reference.pdb"
 fnat_cutoff = 7.0 # cutoff for coarse-grained structures
 
 [cgtoaa]
+log_level = 'verbose'
 
 [emref]
+log_level = 'verbose'
 ambig_fname = "data/ambig.tbl"
 unambig_fname = "data/unambig.tbl"
 randremoval = false

diff --git a/examples/docking-protein-DNA/docking-protein-DNA-cmrest-test.cfg b/examples/docking-protein-DNA/docking-protein-DNA-cmrest-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # protein-DNA docking example
 
-# directory in which the run will be done
+# directory for the run
 run_dir = "run1-cmrest-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-protein-DNA/docking-protein-DNA-mdref-test.cfg b/examples/docking-protein-DNA/docking-protein-DNA-mdref-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # protein-DNA docking example
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-mdref-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-protein-DNA/docking-protein-DNA-test.cfg b/examples/docking-protein-DNA/docking-protein-DNA-test.cfg
@@ -1,12 +1,12 @@
 # ====================================================================
 # protein-DNA docking example
 
-# directory in which the scoring will be done
+# directory for the run
 run_dir = "run1-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules =  [

diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
@@ -5,11 +5,12 @@
 #  (generated with GLYCAM) to an unbound protein.
 # ==================================================
 
+# directory for the run
 run_dir = "run1-flexref-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules = [

diff --git a/examples/docking-protein-glycan/docking-protein-glycan-ilrmsd-test.cfg b/examples/docking-protein-glycan/docking-protein-glycan-ilrmsd-test.cfg
@@ -7,10 +7,13 @@
 #  The IL-RMSD clustering is used here to cluster
 #  complex structures
 # ==================================================
-clean=false
+# directory for the run
+run_dir = "run1-ilrmsd-test"
+
+# execution mode
 mode = "local"
 ncores = 10
-run_dir = "run1-ilrmsd-test"
+
 # list, insert full path
 molecules = [
     "data/1LMQ_r_u.pdb",

diff --git a/examples/docking-protein-glycan/docking-protein-glycan-test.cfg b/examples/docking-protein-glycan/docking-protein-glycan-test.cfg
@@ -5,11 +5,12 @@
 #  (generated with GLYCAM) to an unbound protein.
 # ==================================================
 
+# directory for the run
 run_dir = "run1-test"
 
 # execution mode
 mode = "local"
-ncores = 40
+ncores = 10
 
 # molecules to be docked
 molecules = [