frodock.output-Native

user@NGS-1:/home/nuser/frodock/FRODOCK_v2.0_Linux$ time ./run_frodock_tests.sh
STAGE-1 Creation of receptor vdw potential map
With hydrogens: no
Grid voxel: 1.0
Option: VdW potential. Probe radius: 2.0
Written output potential (VdW or Electrostatic) map: 3hfl_fv_W.ccp4
STAGE-2 Creation of the receptor electrostatic potential map
With hydrogens: no
Grid voxel: 1.0
Option: Electrostatic potential.
Written output potential (VdW or Electrostatic) map: 3hfl_fv_E.ccp4
STAGE-3 Creation of the receptor desolvation potential map
With hydrogens: no
Grid voxel: 1.0
Option: Desolvation potential.
        Radius -> Water: 1.400000 - Generic atom probe: 1.950000

Pre-stage for ASA computation (in_wradprobe= 1.400000)... Finished!
Computing the original ASA in all the 1661 atoms...
ASA pdb file 3hfl_fv_ASA.pdb created (ASA introduced in Occupancy column)
Creating mask volume of invalid positions for the probe (where probe collides with atoms)... Finished!
Computing Solvation Map...
Total ASA computations: 617088  (skipped: 341208  out: 1319168)
STAGE-4 Creation of the ligand desolvation potential map
With hydrogens: no
Grid voxel: 1.0
Option: Desolvation potential.
        Radius -> Water: 1.400000 - Generic atom probe: 1.950000

Pre-stage for ASA computation (in_wradprobe= 1.400000)... Finished!
Computing the original ASA in all the 1001 atoms...
ASA pdb file 3hfl_ly2_ASA.pdb created (ASA introduced in Occupancy column)
Creating mask volume of invalid positions for the probe (where probe collides with atoms)... Finished!
Computing Solvation Map...
Total ASA computations: 383029  (skipped: 207794  out: 821398)
STAGE-5 Performing the docking
frodock> Name H convention: pdb
frodock> Force Field: CHARMM
frodock>
frodock> Reading receptor PDB
frodock>  Receptor accessibility read from receptor PDB
frodock>   ...occupancy column seems to have ASA values
frodock>  Creating Accessibility map from receptor PDB...
frodock>  Accessibility map created from receptor PDB
frodock>
frodock> Receptor VDW map information:
frodock>  Receptor VDW map read from file
frodock>   Map  origin: -33.141129 -39.668289 -12.076756
frodock>   Map  size: 89 81 75
frodock>   Grid size: 1.00 
frodock>
frodock> Receptor electrostatic map information:
frodock>  Receptor electrostatic map read from file
frodock>   Map modification. Threshold applied: 10.000000
frodock>   Map origin: -33.141129 -39.668289 -12.076756
frodock>   Map size: 89 81 75
frodock>
frodock> Receptor desolvation map information:
frodock>  Receptor electrostatic map read from file
frodock>   Map origin: -24.141129 -30.668287 -3.076756
frodock>   Map size: 71 63 57
frodock>
frodock> Reading ligand pdb
frodock>  Ligand center: 39.044571 33.064610 11.924802
frodock>  Ligand accesilibility read from Ligand PDB
frodock>   ....occupancy column seems to have ASA values
frodock>  Ligand desolvation map read from file
frodock>
frodock> Spherical Harmonic setup
frodock>  Receptor vdw radius in A: 71.000000 (71 spherical layers)
frodock>  Ligand vdw radius in A: 25.011627 (26 spherical layers)
frodock>  Receptor max radius in A 33.754642  63.509285
frodock>  Ligand electrostatic radius in A: 25.011627 (26 spherical layers)
frodock>  Ligand accessibility radius in A: 25.011627 (26 spherical layers)
frodock>  Ligand desolvation radius in A: 30.011627 (31 spherical layers)
frodock>  Maximum ligand desolvation radius in A: 30.011627 (31 spherical layers)
frodock>  Precomputation of Ligand spherical representation  Time:  00h. 00' 40''
frodock>
frodock> Determination of translational points to explore
adp_pp> Maximum size of the PDB(in amstrongs): 24.000000
adp_pp> Minimum size of the PDB:(in amstrongs) 10.000000
dilateMax=18.000000 voxel_lig_out[1]=24.000000 limitMaxMask=0.250000
dilateMin=7.000000 voxel_lig_out[0]=10.000000 limitMinMask=0.260000
vol final: 88 77 71
radiusMax_lig_amstrongs_backbone=25.505754frodock>  Mask created
frodock>   Number of points to explore: 20356  saving all best solutions
frodock>
frodock> Searching 100.00
frodock> Number of solutions: 63081 
frodock> Total time:  00h. 57' 27''
frodock>
STAGE-6 Clustering and visualization of predictions
Sort process...
Maximum correlation: 2166.626953 
Clustering process...
STAGE-7 Visualize the first 10 solutions
        1        85.82  158.30  201.32           19.36    6.83   55.42     2166.627
        2       300.26  130.25   89.91            3.36   10.83   49.42     1935.690
        3       243.63   82.85   27.04           11.36    2.83   57.42     1914.379
        4       311.73   79.44  144.35            5.36    2.83   51.42     1908.424
        5       157.72  107.91   72.99           11.36    0.83   53.42     1853.228
        6       116.35   75.06  304.21            9.36    4.83   51.42     1838.161
        7       285.79   50.20  187.66            7.36    8.83   51.42     1833.718
        8       352.14   85.51  198.08           11.36    0.83   57.42     1831.092
        9       245.61   48.21  106.23           15.36    4.83   53.42     1826.980
        10      336.83  117.52   84.76            5.36   10.83   51.42     1817.085
STAGE-8 Coordinate generation of the 5 best predicted solutions
        1        85.82  158.30  201.32           19.36    6.83   55.42     2166.627 => 3hfl_ly2_1.pdb
        2       300.26  130.25   89.91            3.36   10.83   49.42     1935.690 => 3hfl_ly2_2.pdb
        3       243.63   82.85   27.04           11.36    2.83   57.42     1914.379 => 3hfl_ly2_3.pdb
        4       311.73   79.44  144.35            5.36    2.83   51.42     1908.424 => 3hfl_ly2_4.pdb
        5       157.72  107.91   72.99           11.36    0.83   53.42     1853.228 => 3hfl_ly2_5.pdb
TEST FINISHED!
First solution (3hfl_ly2_1.pdb) should match the native structure: 3hfl_ly_ref.pdb

real    67m46.696s
user    67m43.339s
sys     0m5.526s