frodock-native-1a8m_1bj8

nuser@NGS-1:/home/nuser/frodock/FRODOCK_v2.0_Linux$ time ./run_frodock_tests.sh 1a8m  1bj8 pdb_data
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: 1a8m_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: 1a8m_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 3630 atoms...
ASA pdb file 1a8m_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: 1194541  (skipped: 691221  out: 2465662)
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 890 atoms...
ASA pdb file 1bj8_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: 389959  (skipped: 205933  out: 832296)
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: -31.934477 -0.145519 -9.223343
frodock>   Map  size: 105 101 99
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: -31.934477 -0.145519 -9.223343
frodock>   Map size: 105 101 99
frodock>
frodock> Receptor desolvation map information:
frodock>  Receptor electrostatic map read from file
frodock>   Map origin: -22.934477 8.854481 -0.223343
frodock>   Map size: 87 83 81
frodock>
frodock> Reading ligand pdb
frodock>  Ligand center: 15.809546 9.924129 7.932427
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: 89.000000 (89 spherical layers)
frodock>  Ligand vdw radius in A: 34.248821 (35 spherical layers)
frodock>  Receptor max radius in A 42.657120  81.314240
frodock>  Ligand electrostatic radius in A: 34.248821 (35 spherical layers)
frodock>  Ligand accessibility radius in A: 34.248821 (35 spherical layers)
frodock>  Ligand desolvation radius in A: 39.248821 (40 spherical layers)
frodock>  Maximum ligand desolvation radius in A: 39.248821 (40 spherical layers)
frodock>  Precomputation of Ligand spherical representation  Time:  00h. 00' 43''
frodock>
frodock> Determination of translational points to explore
adp_pp> Maximum size of the PDB(in amstrongs): 31.000000
adp_pp> Minimum size of the PDB:(in amstrongs) 9.000000
dilateMax=23.000000 voxel_lig_out[1]=31.000000 limitMaxMask=0.250000
dilateMin=6.000000 voxel_lig_out[0]=9.000000 limitMinMask=0.260000
vol final: 105 106 103
radiusMax_lig_amstrongs_backbone=32.129639frodock>  Mask created
frodock>   Number of points to explore: 51890  saving all best solutions
frodock>
frodock> Searching  85.92
frodock> Searching 100.00
frodock> Number of solutions: 176905 
frodock> Total time:  02h. 43' 40''
frodock>
STAGE-6 Clustering and visualization of predictions
Sort process...
Maximum correlation: 1569.087280 
Clustering process...
STAGE-7 Visualize the first 10 solutions
        1       105.24   94.52  157.59           18.57   84.35   46.28     1569.087
        2       224.19  130.31   62.22           28.57   64.35   70.28     1513.503
        3       251.14   88.47  236.97           48.57   44.35   18.28     1506.992
        4       265.87   41.75   23.85           40.57   80.35   42.28     1482.536
        5        31.07  164.22   98.06           26.57   64.35   70.28     1476.852
        6       211.60  128.11   79.72           36.57   54.35   74.28     1476.085
        7        54.85  118.78  300.50            0.57   20.35   42.28     1440.536
        8       253.44   95.49  313.39           28.57   80.35   26.28     1377.873
        9       110.74   84.74  164.74           20.57   84.35   42.28     1375.999
        10        2.10   55.70  187.02           -9.43   50.35   14.28     1366.804
STAGE-8 Coordinate generation of the 5 best predicted solutions
        1       105.24   94.52  157.59           18.57   84.35   46.28     1569.087 => 1bj8_1.pdb
        2       224.19  130.31   62.22           28.57   64.35   70.28     1513.503 => 1bj8_2.pdb
        3       251.14   88.47  236.97           48.57   44.35   18.28     1506.992 => 1bj8_3.pdb
        4       265.87   41.75   23.85           40.57   80.35   42.28     1482.536 => 1bj8_4.pdb
        5        31.07  164.22   98.06           26.57   64.35   70.28     1476.852 => 1bj8_5.pdb
TEST FINISHED!
First solution (1bj8_1.pdb) should match the native structure: 3hfl_ly_ref.pdb

real    180m11.015s
user    180m2.549s
sys     0m16.556s