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"