[Swift-commit] r8270 - in SwiftApps/subjobs: . dock rosetta
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Thu Oct 9 17:30:29 CDT 2014
Author: ketan
Date: 2014-10-09 17:30:29 -0500 (Thu, 09 Oct 2014)
New Revision: 8270
Added:
SwiftApps/subjobs/dock/
SwiftApps/subjobs/dock/apps
SwiftApps/subjobs/dock/cf
SwiftApps/subjobs/dock/cobalt.xml
SwiftApps/subjobs/dock/dock.swift
SwiftApps/subjobs/dock/dock_mpi.in
SwiftApps/subjobs/dock/flex.defn
SwiftApps/subjobs/dock/flex_drive.tbl
SwiftApps/subjobs/dock/vdw_AMBER_parm99.defn
SwiftApps/subjobs/dock/zinc_nci_0010.mol2
Modified:
SwiftApps/subjobs/rosetta/rosetta.swift
Log:
add dock and a small change to rosetta
Added: SwiftApps/subjobs/dock/apps
===================================================================
--- SwiftApps/subjobs/dock/apps (rev 0)
+++ SwiftApps/subjobs/dock/apps 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,3 @@
+localhost cat /bin/cat null null null
+cluster bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null
+
Added: SwiftApps/subjobs/dock/cf
===================================================================
--- SwiftApps/subjobs/dock/cf (rev 0)
+++ SwiftApps/subjobs/dock/cf 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,6 @@
+use.provider.staging=false
+wrapperlog.always.transfer=false
+execution.retries=0
+provider.staging.pin.swiftfiles=false
+sitedir.keep=false
+use.wrapper.staging=false
Added: SwiftApps/subjobs/dock/cobalt.xml
===================================================================
--- SwiftApps/subjobs/dock/cobalt.xml (rev 0)
+++ SwiftApps/subjobs/dock/cobalt.xml 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+
+<pool handle="cluster">
+<execution provider="coaster" jobmanager="local:cobalt" />
+
+<profile namespace="globus" key="slots">2</profile>
+<profile namespace="globus" key="mode">script</profile>
+
+<profile namespace="karajan" key="jobThrottle">2.99</profile>
+<profile namespace="karajan" key="initialScore">10000</profile>
+<profile namespace="globus" key="maxwalltime">00:40:00</profile>
+<profile namespace="globus" key="walltime">2050</profile>
+
+<profile namespace="globus" key="maxnodes">256</profile>
+<profile namespace="globus" key="nodegranularity">256</profile>
+<profile key="SUBBLOCK_SIZE" namespace="env">16</profile>
+<profile key="WORKER_LOGGING_LEVEL" namespace="env">DEBUG</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">TRUE</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">ON</profile>
+<profile key="WORKER_LOG_DIR" namespace="env">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+<profile namespace="globus" key="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="jobsPerNode">16</profile>
+
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<filesystem provider="local"/>
+
+</pool>
+</config>
Added: SwiftApps/subjobs/dock/dock.swift
===================================================================
--- SwiftApps/subjobs/dock/dock.swift (rev 0)
+++ SwiftApps/subjobs/dock/dock.swift 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,21 @@
+type file;
+
+// Dock
+app (file _dockoutfile, file out, file err) dock (file _dockinfile)
+{
+ bgsh "/home/ketan/dock6/bin/dock" "-i" @_dockinfile "-o" @_dockoutfile stdout=@out stderr=@err;
+}
+
+// Files
+file infiles[] <filesys_mapper; location="dock_infiles", suffix=".in">;
+file logs[];
+
+// Run scaling tests
+foreach infile,i in infiles {
+ file dock_output <single_file_mapper; file=strcat("logs/dock.", i, ".out")>;
+ file dock_error <single_file_mapper; file=strcat("logs/dock.", i, ".err")>;
+ file dockoutfile <single_file_mapper; file=strcat("dock.",i, ".sc")>;
+ (dockoutfile, dock_output, dock_error) = dock(pdb, 2);
+ logs[i] = dock_output;
+}
+
Added: SwiftApps/subjobs/dock/dock_mpi.in
===================================================================
--- SwiftApps/subjobs/dock/dock_mpi.in (rev 0)
+++ SwiftApps/subjobs/dock/dock_mpi.in 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,66 @@
+ligand_atom_file zinc_nci_0010.mol2
+limit_max_ligands no
+skip_molecule no
+read_mol_solvation no
+calculate_rmsd no
+use_database_filter no
+orient_ligand yes
+automated_matching yes
+receptor_site_file rec.10A.sph
+max_orientations 500
+critical_points no
+chemical_matching no
+use_ligand_spheres no
+use_internal_energy yes
+internal_energy_rep_exp 12
+flexible_ligand yes
+user_specified_anchor no
+limit_max_anchors no
+min_anchor_size 40
+pruning_use_clustering yes
+pruning_max_orients 100
+pruning_clustering_cutoff 100
+pruning_conformer_score_cutoff 25.0
+use_clash_overlap no
+write_growth_tree no
+bump_filter no
+score_molecules yes
+contact_score_primary no
+contact_score_secondary no
+grid_score_primary yes
+grid_score_secondary no
+grid_score_rep_rad_scale 1
+grid_score_vdw_scale 1
+grid_score_es_scale 1
+grid_score_grid_prefix 1VRT.rec
+multigrid_score_secondary no
+dock3.5_score_secondary no
+continuous_score_secondary no
+descriptor_score_secondary no
+gbsa_zou_score_secondary no
+gbsa_hawkins_score_secondary no
+SASA_descriptor_score_secondary no
+amber_score_secondary no
+minimize_ligand yes
+minimize_anchor yes
+minimize_flexible_growth yes
+use_advanced_simplex_parameters no
+simplex_max_cycles 1
+simplex_score_converge 0.1
+simplex_cycle_converge 1.0
+simplex_trans_step 1.0
+simplex_rot_step 0.1
+simplex_tors_step 10.0
+simplex_anchor_max_iterations 500
+simplex_grow_max_iterations 500
+simplex_grow_tors_premin_iterations 0
+simplex_random_seed 0
+simplex_restraint_min no
+atom_model all
+vdw_defn_file vdw_AMBER_parm99.defn
+flex_defn_file flex.defn
+flex_drive_file flex_drive.tbl
+ligand_outfile_prefix 1VRT
+write_orientations no
+num_scored_conformers 1
+rank_ligands no
Added: SwiftApps/subjobs/dock/flex.defn
===================================================================
--- SwiftApps/subjobs/dock/flex.defn (rev 0)
+++ SwiftApps/subjobs/dock/flex.defn 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,288 @@
+5/98 te
+11/98 kb, ags, mll
+3/0 kb
+______________________________________________________________________
+name sp3-sp3
+drive_id 3
+minimize 1
+
+definition .3 [ 3 H ]
+definition .3 [ 3 H ]
+______________________________________________________________________
+name sp3-sp2
+drive_id 6
+minimize 1
+
+definition .3 [ 3 H ]
+definition .2 [ 2 H ]
+______________________________________________________________________
+name sp3-aromatic
+drive_id 6
+minimize 1
+
+definition .3 [ 3 H ]
+definition .ar
+______________________________________________________________________
+name sp3-n4
+drive_id 3
+minimize 1
+
+definition .3 [ 3 H ]
+definition N.4 [ 3 H ]
+______________________________________________________________________
+name sp3-npl
+drive_id 6
+minimize 1
+
+definition .3 [ 3 H ]
+definition N.pl3
+______________________________________________________________________
+name sp3-n_amide
+drive_id 6
+minimize 1
+
+definition .3 [ 3 H ]
+definition N.am
+______________________________________________________________________
+name sp3-sp1
+drive_id 3
+minimize 1
+
+definition .3 [ 3 H ]
+definition .1 ( . )
+______________________________________________________________________
+name sp2-sp2
+drive_id 2
+minimize 0
+
+definition .2 [ 2 H ]
+definition .2 [ 2 H ]
+______________________________________________________________________
+name sp2-aromatic
+drive_id 2
+minimize 0
+
+definition .2 [ 2 H ]
+definition .ar
+______________________________________________________________________
+name sp2-n4
+drive_id 6
+minimize 1
+
+definition .2 [ 2 H ]
+definition N.4 [ 3 H ]
+______________________________________________________________________
+name sp2-npl
+drive_id 2
+minimize 0
+
+definition .2 [ 2 H ]
+definition N.pl3
+______________________________________________________________________
+name sp2-n_amide
+drive_id 2
+minimize 0
+
+definition .2 [ 2 H ]
+definition N.am
+______________________________________________________________________
+
+SPECIAL CASES COME LAST TO SUPERCEDE GENERAL DEFINITIONS
+______________________________________________________________________
+name npl3-aromatic
+drive_id 2
+minimize 0
+
+definition N.pl3 [ 2 H ] [ 2 O ]
+definition .ar
+______________________________________________________________________
+name n_amide-n_amide
+drive_id 2
+minimize 0
+
+definition N.am
+definition N.am
+______________________________________________________________________
+name n_amide-aromatic
+drive_id 2
+minimize 0
+
+definition N.am
+definition .ar
+______________________________________________________________________
+name acetyl-sp2
+drive_id 2
+minimize 1
+
+definition C.2 ( O.2 ) ( C.3 )
+definition .2 [ 2 H ]
+______________________________________________________________________
+name ccat-n
+drive_id 2
+minimize 0
+
+definition C.cat
+definition N [ 2 H ]
+______________________________________________________________________
+name carboxyl-sp3
+drive_id 62
+minimize 1
+
+definition C.2 ( 2 O.co2 )
+definition .3 [ 3 H ]
+______________________________________________________________________
+name arom-oxygen
+drive_id 2
+minimize 1
+
+definition O.3 [ H ]
+definition C.ar
+______________________________________________________________________
+name conj-oxygen
+drive_id 2
+minimize 0
+
+definition O.3 [ H ]
+definition .2 [ 2 H ]
+______________________________________________________________________
+name arom-sulfur
+drive_id 2
+minimize 1
+
+definition S.3 [ H ]
+definition C.ar
+______________________________________________________________________
+name conj-sulfur
+drive_id 2
+minimize 0
+
+definition S.3 [ H ]
+definition .2 [ 2 H ]
+______________________________________________________________________
+name ester
+drive_id 2
+minimize 0
+
+definition C.2 ( O.2 )
+definition O.3 ( . )
+______________________________________________________________________
+name sulfyl-ester
+drive_id 2
+minimize 0
+
+definition C.2 ( S.2 )
+definition S.3 ( . )
+______________________________________________________________________
+name arom-hydroxyl
+drive_id 2
+minimize 1
+
+definition O.3 ( H )
+definition C.ar
+______________________________________________________________________
+name conj-hydroxyl
+drive_id 2
+minimize 1
+
+definition O.3 ( H )
+definition .2
+______________________________________________________________________
+name arom-hydrosulfyl
+drive_id 2
+minimize 1
+
+definition S.3 ( H )
+definition C.ar
+______________________________________________________________________
+name conj-hydrosulfyl
+drive_id 2
+minimize 1
+
+definition S.3 ( H )
+definition .2 [ 2 H ]
+______________________________________________________________________
+name phosph-ester
+drive_id 62
+minimize 1
+
+definition P.3 ( 2 O.co2 )
+definition O.3
+______________________________________________________________________
+name sulfate-ester
+drive_id 62
+minimize 1
+
+definition S ( 4 O )
+definition O.3
+______________________________________________________________________
+name sulfonate-arom
+drive_id 63
+minimize 1
+
+definition S ( 3 O [ * ] )
+definition C.ar
+______________________________________________________________________
+name sulfonate-sp2
+drive_id 63
+minimize 0
+
+definition S ( 3 O [ * ] )
+definition .2 [ 2 H ]
+______________________________________________________________________
+name sulfonamide
+drive_id 3
+minimize 1
+
+definition S ( 2 O [ * ] )
+definition N
+______________________________________________________________________
+name aromatic_sulfonamide
+drive_id 32
+minimize 1
+
+definition S ( 2 O [ * ] ) ( C.ar )
+definition N [ 2 H ]
+______________________________________________________________________
+name sulfone-sp3
+drive_id 3
+minimize 1
+
+definition S ( 2 O [ * ] )
+definition .3 [ 3 H ]
+______________________________________________________________________
+name sulfone-sp2
+drive_id 6
+minimize 1
+
+definition S ( 2 O [ * ] )
+definition .2 [ 2 H ]
+______________________________________________________________________
+name sulfone-aromatic
+drive_id 122
+minimize 1
+
+definition S ( 2 O [ * ] )
+definition C.ar [ 2 H ]
+______________________________________________________________________
+name silicon-sp3
+drive_id 6
+minimize 1
+
+definition Si [ 3 H ]
+definition .3 [ 3 H ]
+______________________________________________________________________
+name silicon-oxygen
+drive_id 3
+minimize 1
+
+definition Si [ 3 H ]
+definition O.3
+______________________________________________________________________
+name amide
+drive_id 1
+minimize 0
+
+definition N.am ( H )
+definition C.2 ( O.2 )
+______________________________________________________________________
+
Added: SwiftApps/subjobs/dock/flex_drive.tbl
===================================================================
--- SwiftApps/subjobs/dock/flex_drive.tbl (rev 0)
+++ SwiftApps/subjobs/dock/flex_drive.tbl 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,41 @@
+________________________________________________________
+drive_id 1
+positions 1
+torsions 180
+________________________________________________________
+drive_id 2
+positions 2
+torsions 0 180
+________________________________________________________
+drive_id 3
+positions 3
+torsions -60 60 180
+________________________________________________________
+drive_id 32
+positions 2
+torsions -60 60
+________________________________________________________
+drive_id 4
+positions 4
+torsions -90 0 90 180
+________________________________________________________
+drive_id 6
+positions 6
+torsions -150 -90 -30 30 90 150
+________________________________________________________
+drive_id 62
+positions 3
+torsions -90 -30 30
+________________________________________________________
+drive_id 63
+positions 2
+torsions -30 30
+________________________________________________________
+drive_id 8
+positions 8
+torsions -135 -90 -45 0 45 90 135 180
+________________________________________________________
+drive_id 122
+positions 6
+torsions -120 -90 -60 60 90 120
+________________________________________________________
Added: SwiftApps/subjobs/dock/vdw_AMBER_parm99.defn
===================================================================
--- SwiftApps/subjobs/dock/vdw_AMBER_parm99.defn (rev 0)
+++ SwiftApps/subjobs/dock/vdw_AMBER_parm99.defn 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,472 @@
+___________________________________________________________________________
+
+
+ AMBER99-based Lennard-Jones parameters for van der Waals
+ energy potential.
+
+
+ The radius corresponds to half the equilibrium distance
+ (in Angstroms) between atoms.
+
+ The well depth corresponds to the energy (in kcal/mol)
+ at the equilibrium distance.
+
+ Lennard-Jones parameters are derived as follows:
+
+ sqrt(A) = sqrt [e * b/(a-b) * (2r)^a]
+ sqrt(B) = sqrt [e * a/(a-b) * (2r)^b]
+
+ where:
+ r = radius
+ e = well depth
+ a = repulsive exponent
+ b = attractive exponent
+
+
+ P. Therese Downing (07/02)
+ Robert Rizzo (06/05) added radii for GB calculations
+ P. Therese Lang (07/06): added full list of Aqvist ions
+ (J. Phys. Chem. v94 p8021).
+___________________________________________________________________________
+
+_____________________________________
+name Carbon
+atom_model either
+radius 1.908
+well_depth 0.086
+heavy_flag 1
+valence 4
+gbradii 1.70
+gbscale 0.72
+
+definition C
+_____________________________________
+name Carbon_All_sp3
+atom_model all
+radius 1.908
+well_depth 0.1094
+heavy_flag 1
+valence 4
+gbradii 1.70
+gbscale 0.72
+
+definition C.3
+_____________________________________
+name Hydrogen
+atom_model either
+radius 0.600
+well_depth 0.0157
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H
+_____________________________________
+name Hydrogen_hydroxyl
+atom_model either
+radius 0.1
+well_depth 0.001
+heavy_flag 0
+valence 1
+gbradii 0.80
+gbscale 0.85
+
+definition H ( O )
+_____________________________________
+name Hydrogen_thiol
+atom_model all
+radius 0.600
+well_depth 0.0157
+heavy_flag 0
+valence 1
+gbradii 0.80
+gbscale 0.85
+
+definition H ( S )
+_____________________________________
+name Hydrogen_Aliphatic
+atom_model all
+radius 1.487
+well_depth 0.0157
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.3 )
+_____________________________________
+name Hydrogen_Semipolar
+atom_model all
+radius 1.387
+well_depth 0.0157
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.3 ( O ) )
+definition H ( C.3 ( N ) )
+definition H ( C.3 ( S ) )
+definition H ( C.3 ( F ) )
+definition H ( C.3 ( Cl ) )
+definition H ( C.3 ( Br ) )
+_____________________________________
+name Hydrogen_2_Semipolar
+atom_model all
+radius 1.287
+well_depth 0.0157
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.3 ( 2 O) )
+definition H ( C.3 ( 2 N) )
+definition H ( C.3 ( 2 S) )
+definition H ( C.3 ( N ) ( O ) )
+definition H ( C.3 ( S ) ( O ) )
+definition H ( C.3 ( S ) ( N ) )
+definition H ( C.3 ( 2 F ) )
+definition H ( C.3 ( 2 Cl ) )
+definition H ( C.3 ( 2 Br ) )
+_____________________________________
+name Hydrogen_1-3_Charged
+atom_model all
+radius 1.100
+well_depth 0.0157
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.3 ( N.4 ) )
+_____________________________________
+name Hydrogen_sp2
+atom_model all
+radius 1.459
+well_depth 0.0150
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.ar )
+definition H ( C.2 )
+_____________________________________
+name Hydrogen_Ar_Sp
+atom_model all
+radius 1.409
+well_depth 0.0150
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.ar ( O ) )
+definition H ( C.ar ( N ) )
+definition H ( C.2 ( O ) )
+definition H ( C.2 ( N ) )
+_____________________________________
+name Hydrogen_Ar_2_Sp
+atom_model all
+radius 1.359
+well_depth 0.0150
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.ar ( 2 O ) )
+definition H ( C.ar ( 2 N ) )
+definition H ( C.ar ( N ) ( O ) )
+definition H ( C.2 ( 2 O ) )
+definition H ( C.2 ( 2 N ) )
+definition H ( C.2 ( N ) ( O ) )
+_____________________________________
+name Hydrogen_alkyne
+atom_model all
+radius 1.459
+well_depth 0.015
+heavy_flag 0
+valence 1
+gbradii 1.30
+gbscale 0.85
+
+definition H ( C.1 )
+_____________________________________
+name Nitrogen
+atom_model either
+radius 1.824
+well_depth 0.170
+heavy_flag 1
+valence 4
+gbradii 1.55
+gbscale 0.79
+
+definition N
+_____________________________________
+name Oxygen
+atom_model either
+radius 1.6612
+well_depth 0.210
+heavy_flag 1
+valence 2
+gbradii 1.50
+gbscale 0.85
+
+definition O
+_____________________________________
+name Oxygen_ether
+atom_model either
+radius 1.6837
+well_depth 0.170
+heavy_flag 1
+valence 2
+gbradii 1.50
+gbscale 0.85
+
+definition O.3
+_____________________________________
+name Oxygen_alcohol
+atom_model either
+radius 1.721
+well_depth 0.2104
+heavy_flag 1
+valence 2
+gbradii 1.50
+gbscale 0.85
+
+definition O.3 ( H )
+_____________________________________
+name Oxygen_TIP3_water
+atom_model all
+radius 1.7683
+well_depth 0.1520
+heavy_flag 1
+valence 2
+gbradii 1.50
+gbscale 0.85
+
+definition O.3 ( 2 H )
+_____________________________________
+name Sulfur
+atom_model either
+radius 2.000
+well_depth 0.250
+heavy_flag 1
+valence 6
+gbradii 1.80
+gbscale 0.96
+
+definition S
+_____________________________________
+name Phosphorus
+atom_model either
+radius 2.100
+well_depth 0.200
+heavy_flag 1
+valence 5
+gbradii 1.85
+gbscale 0.86
+
+definition P
+_____________________________________
+name Fluorine
+atom_model either
+radius 1.750
+well_depth 0.061
+heavy_flag 1
+valence 1
+gbradii 1.50
+gbscale 0.88
+
+definition F
+_____________________________________
+name Chlorine
+atom_model either
+radius 1.948
+well_depth 0.265
+heavy_flag 1
+valence 1
+gbradii 1.70
+gbscale 0.80
+
+definition Cl
+_____________________________________
+name Bromine
+atom_model either
+radius 2.220
+well_depth 0.320
+heavy_flag 1
+valence 4
+gbradii 1.85
+gbscale 0.80
+
+definition Br
+_____________________________________
+name Silicon
+atom_model either
+radius 2.220
+well_depth 0.320
+heavy_flag 1
+valence 4
+gbradii 2.10
+gbscale 0.80
+
+definition Si
+_____________________________________
+name Iodine
+atom_model either
+radius 2.350
+well_depth 0.400
+heavy_flag 1
+valence 1
+gbradii 1.98
+gbscale 0.80
+
+definition I
+_____________________________________
+name Potassium+
+atom_model either
+radius 2.658
+well_depth 0.000328
+heavy_flag 1
+valence 0
+gbradii 2.75
+gbscale 0.80
+
+definition K
+_____________________________________
+name Sodium+
+atom_model either
+radius 1.868
+well_depth 0.00277
+heavy_flag 1
+valence 1
+gbradii 2.27
+gbscale 0.80
+
+definition Na
+_____________________________________
+name Mg++
+atom_model either
+radius 0.787
+well_depth 0.875
+heavy_flag 1
+valence 6
+gbradii 1.73
+gbscale 0.80
+
+definition Mg
+_____________________________________
+name Li+
+atom_model either
+radius 1.137
+well_depth 0.0183
+heavy_flag 1
+valence 0
+gbradii 1.82
+gbscale 0.80
+
+definition Li
+_____________________________________
+name Rubidium
+atom_model all
+radius 2.956
+well_depth 0.00017
+heavy_flag 1
+valence 1
+gbradii 0.000
+gbscale 0.000
+
+definition Rb
+_____________________________________
+name Cesium
+atom_model all
+radius 3.395
+well_depth 0.0000806
+heavy_flag 1
+valence 1
+gbradii 0.000
+gbscale 0.000
+
+definition Cs
+____________________________________
+name Calcium2+
+atom_model all
+radius 1.326
+well_depth 0.4497
+heavy_flag 1
+valence 10
+gbradii 1.70
+gbscale 0.72
+
+definition Ca
+____________________________________
+name Zinc
+atom_model all
+radius 1.10
+well_depth 0.0125
+heavy_flag 1
+valence 8
+gbradii 1.39
+gbscale 0.80
+
+definition Zn
+_____________________________________
+name Iron
+atom_model all
+radius 1.2
+well_depth 0.05
+heavy_flag 1
+valence 8
+gbradii 1.50
+gbscale 0.80
+
+definition Fe
+_____________________________________
+name Strontium++
+atom_model all
+radius 1.742
+well_depth 0.118
+heavy_flag 1
+valence 8
+gbradii 0.00
+gbscale 0.00
+
+definition Sr
+_____________________________________
+name Barium++
+atom_model all
+radius 2.124
+well_depth 0.047
+heavy_flag 1
+valence 8
+gbradii 0.00
+gbscale 0.00
+
+definition Ba
+_____________________________________
+name Vanadium
+atom_model either
+radius 2.100
+well_depth 0.320
+heavy_flag 1
+valence 6
+gbradii 1.50
+gbscale 0.80
+
+definition V
+_____________________________________
+name Dummy
+atom_model either
+radius 0.000
+well_depth 0.000
+heavy_flag 0
+valence 10
+gbradii 0.000
+gbscale 0.000
+
+definition Du
+_____________________________________
Added: SwiftApps/subjobs/dock/zinc_nci_0010.mol2
===================================================================
--- SwiftApps/subjobs/dock/zinc_nci_0010.mol2 (rev 0)
+++ SwiftApps/subjobs/dock/zinc_nci_0010.mol2 2014-10-09 22:30:29 UTC (rev 8270)
@@ -0,0 +1,542 @@
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+########## Name : 1VRT.lig
+########## Description : AM1BCC_CHARGES = -0.0002 ORIGINAL_CHARGES = -0.0000
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+20 N4 1.7670 -37.6730 21.8260 N.pl3 1 LIG -0.6924 -0.3690
+21 C11 2.7540 -36.8570 22.5840 C.ar 1 LIG 0.5805 0.4100
+22 C12 2.9040 -34.5090 25.6010 C.3 1 LIG -0.0620 0.1435
+23 H7 2.2235 -33.7630 25.2820 H 1 LIG 0.0570 0.0000
+24 H8 2.4436 -35.1154 26.3371 H 1 LIG 0.0495 0.0000
+25 H9 3.7654 -34.0491 26.0108 H 1 LIG 0.0519 0.0000
+26 O1 -1.2400 -35.9060 23.9770 O.2 1 LIG -0.6361 -0.5700
+27 C13 2.3440 -38.7570 21.0360 C.3 1 LIG 0.1354 0.0690
+28 H10 3.1238 -38.3754 20.4296 H 1 LIG 0.0981 0.1000
+29 C14 2.9380 -39.8900 21.8010 C.3 1 LIG -0.1181 -0.2000
+30 H11 3.8890 -40.1268 21.3997 H 1 LIG 0.0732 0.1000
+31 H12 3.0430 -39.6129 22.8177 H 1 LIG 0.0789 0.1000
+32 C15 1.6390 -40.0610 21.0880 C.3 1 LIG -0.1196 -0.2000
+33 H13 0.6832 -39.9283 21.5242 H 1 LIG 0.0807 0.1000
+34 H14 1.5292 -40.4423 20.1061 H 1 LIG 0.0733 0.1000
+@<TRIPOS>BOND
+1 2 1 ar
+2 3 2 1
+3 4 2 ar
+4 5 4 1
+5 6 4 ar
+6 7 6 ar
+7 8 7 1
+8 9 8 1
+9 10 8 1
+10 11 10 1
+11 12 11 ar
+12 13 12 1
+13 14 12 ar
+14 15 14 1
+15 16 14 ar
+16 17 16 1
+17 18 16 ar
+18 19 11 ar
+19 19 18 ar
+20 20 19 1
+21 21 1 ar
+22 21 7 ar
+23 21 20 1
+24 22 6 1
+25 23 22 1
+26 24 22 1
+27 25 22 1
+28 26 10 2
+29 27 20 1
+30 28 27 1
+31 29 27 1
+32 30 29 1
+33 31 29 1
+34 32 27 1
+35 32 29 1
+36 33 32 1
+37 34 32 1
+@<TRIPOS>SUBSTRUCTURE
+1 LIG 1
+
Modified: SwiftApps/subjobs/rosetta/rosetta.swift
===================================================================
--- SwiftApps/subjobs/rosetta/rosetta.swift 2014-10-09 18:03:59 UTC (rev 8269)
+++ SwiftApps/subjobs/rosetta/rosetta.swift 2014-10-09 22:30:29 UTC (rev 8270)
@@ -12,8 +12,8 @@
// Run scaling tests
foreach pdb,i in pdb_files {
- file rosetta_output <single_file_mapper; file=strcat("logs/h0scale.", i, ".out")>;
- file rosetta_error <single_file_mapper; file=strcat("logs/h0scale.", i, ".err")>;
+ file rosetta_output <single_file_mapper; file=strcat("logs/rosetta.", i, ".out")>;
+ file rosetta_error <single_file_mapper; file=strcat("logs/rosetta.", i, ".err")>;
file scorefile <single_file_mapper; file=strcat("score.",i, ".sc")>;
(scorefile, rosetta_output, rosetta_error) = rosetta(pdb, 2);
//logs[i] = rosetta_output;
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