implement coarse-grain

examples/docking-protein-protein-CG/docking-protein-protein-CG-full.cfg

@@ -0,0 +1,68 @@
+# ====================================================================
+# Protein-protein docking example with NMR-derived ambiguous interaction restraints
+# ====================================================================
+
+# directory in which the scoring will be done
+run_dir = "run1"
+
+# execution mode
+mode = "local"
+
+# molecules to be docked
+molecules =  [
+    "data/e2a_1F3G.pdb",
+    "data/hpr_ensemble_B.pdb"
+    ]
+
+postprocess = false
+
+# ====================================================================
+# Parameters for each stage are defined below, prefer full paths
+# ====================================================================
+
+[topoaa]
+autohis = true
+
+[topocg]
+cgffversion = "martini2"
+
+[rigidbody]
+ambig_fname = "data/e2a-hpr_air.tbl"
+tolerance = 5
+sampling = 1000
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+fnat_cutoff = 7.0 # cutoff for coarse-grained structures
+
+[seletop]
+select = 400
+
+[flexref]
+ambig_fname = "data/e2a-hpr_air.tbl"
+tolerance = 5
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+fnat_cutoff = 7.0 # cutoff for coarse-grained structures
+
+[clustfcc]
+contact_distance_cutoff = 7.0 # cutoff for coarse-grained structures
+
+[seletop]
+select = 200
+
+[cgtoaa]
+log_level = "verbose"
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+
+[emref]
+ambig_fname = "data/e2a-hpr_air.tbl"
+tolerance = 5
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+
+# ====================================================================

examples/docking-protein-protein-CG/docking-protein-protein-CG-test.cfg

@@ -0,0 +1,63 @@
+# ====================================================================
+# Protein-protein docking example with NMR-derived ambiguous interaction restraints
+# ====================================================================
+
+# directory in which the scoring will be done
+run_dir = "run1"
+
+debug = True
+
+# molecules to be docked
+molecules =  [
+    "data/e2a_1F3G.pdb",
+    "data/hpr_ensemble_B.pdb"
+    ]
+
+# ====================================================================
+# Parameters for each stage are defined below, prefer full paths
+# ====================================================================
+
+[topoaa]
+autohis = true
+
+[topocg]
+cgffversion = "martini2"
+
+[rigidbody]
+ambig_fname = "data/e2a-hpr_air.tbl"
+tolerance = 5
+sampling = 10
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+fnat_cutoff = 7.0 # cutoff for coarse-grained structures
+
+[seletop]
+select = 2
+
+[flexref]
+ambig_fname = "data/e2a-hpr_air.tbl"
+tolerance = 5
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+fnat_cutoff = 7.0 # cutoff for coarse-grained structures
+
+[clustfcc]
+min_population = 1
+contact_distance_cutoff = 7.0 # cutoff for coarse-grained structures
+
+[cgtoaa]
+log_level = "verbose"
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+
+[emref]
+ambig_fname = "data/e2a-hpr_air.tbl"
+tolerance = 5
+
+[caprieval]
+reference_fname = "data/e2a-hpr_1GGR.pdb"
+
+# ====================================================================