From 70146158db73dfc1ae0c0df2db3574451dc4892b Mon Sep 17 00:00:00 2001
From: rversini <rapha.versini@gmail.com>
Date: Mon, 13 Apr 2026 18:13:26 +0200
Subject: [PATCH] docking configuration files for all-atom and coarse-grained
 pipeline

---
 .../docking-unbound_benchmark_AA.cfg          | 65 +++++++++++++++++
 .../docking-unbound_benchmark_CG.cfg          | 72 +++++++++++++++++++
 2 files changed, 137 insertions(+)
 create mode 100644 haddock3-scripts/docking-unbound_benchmark_AA.cfg
 create mode 100644 haddock3-scripts/docking-unbound_benchmark_CG.cfg

diff --git a/haddock3-scripts/docking-unbound_benchmark_AA.cfg b/haddock3-scripts/docking-unbound_benchmark_AA.cfg
new file mode 100644
index 0000000..00b87c8
--- /dev/null
+++ b/haddock3-scripts/docking-unbound_benchmark_AA.cfg
@@ -0,0 +1,65 @@
+# ====================================================================
+# Protein-DNA docking benchmark configuration file
+# ====================================================================
+
+# directory in which docking will be done
+run_dir = run-AA-XX
+
+# execution mode
+mode = "local"
+ncores = 80
+debug = true
+
+# molecules to be docked
+molecules = [
+    "XX_p?_u.pdb",
+    "XX_d_u.pdb"
+]
+
+
+
+# ====================================================================
+# Parameters for each stage are defined below; prefer full paths
+# ====================================================================
+
+[topoaa]
+
+[rigidbody]
+tolerance = 90
+ambig_fname = "XX_u_ambig.tbl"
+sampling = 1000
+epsilon = 78
+dielec = "cdie"
+w_desolv = 0
+
+[caprieval]
+reference_fname = "XX_target.pdb"
+
+[seletop]
+select = 200
+
+[flexref]
+tolerance = 90
+ambig_fname = "XX_u_ambig.tbl"
+epsilon = 78
+dielec = "cdie"
+dnarest_on = true
+w_desolv = 0
+
+[caprieval]
+reference_fname = "XX_target.pdb"
+
+[emref]
+ambig_fname = "XX_u_ambig.tbl"
+dnarest_on = true
+w_desolv = 0
+
+[caprieval]
+reference_fname = "XX_target.pdb"
+
+[clustfcc]
+
+[seletopclusts]
+
+[caprieval]
+reference_fname = "XX_target.pdb"
diff --git a/haddock3-scripts/docking-unbound_benchmark_CG.cfg b/haddock3-scripts/docking-unbound_benchmark_CG.cfg
new file mode 100644
index 0000000..cce520e
--- /dev/null
+++ b/haddock3-scripts/docking-unbound_benchmark_CG.cfg
@@ -0,0 +1,72 @@
+# ====================================================================
+# Protein-DNA docking benchmark configuration file
+# ====================================================================
+
+# directory in which docking will be done
+run_dir = run-CG-XX
+
+# execution mode
+mode = "local"
+ncores = 80
+debug = true
+
+# molecules to be docked
+molecules = [
+    "XX_p?_u.pdb",
+    "XX_d_u.pdb"
+]
+
+
+
+# ====================================================================
+# Parameters for each stage are defined below; prefer full paths
+# ====================================================================
+
+[topoaa]
+
+[topocg]
+cgffversion = "martini2"
+
+[rigidbody]
+tolerance = 90
+ambig_fname = "XX_u_ambig.tbl"
+epsilon = 78
+dielec = "cdie"
+w_desolv = 0
+sampling = 1000
+
+[caprieval]
+fnat_cutoff = 7.0 # CG cutoff
+reference_fname = "XX_target.pdb"
+
+[seletop]
+select = 200
+
+[flexref]
+tolerance = 90
+ambig_fname = "XX_u_ambig.tbl"
+epsilon = 78
+dielec = "cdie"
+dnarest_on = true
+w_desolv = 0
+
+[caprieval]
+fnat_cutoff = 7.0 # CG cutoff
+reference_fname = "XX_target.pdb"
+
+[cgtoaa]
+
+[emref]
+ambig_fname = "XX_u_ambig.tbl"
+dnarest_on = true
+w_desolv = 0
+
+[caprieval]
+reference_fname = "XX_target.pdb"
+
+[clustfcc] 
+
+[seletopclusts]
+
+[caprieval]
+reference_fname = "XX_target.pdb"