Created
January 30, 2016 21:49
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ubuntu@ip-172-31-5-104:~/FRODOCK_v2.0_Linux$ ./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 | |
real 0m12.466s | |
user 0m12.458s | |
sys 0m0.008s | |
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 | |
real 0m18.619s | |
user 0m18.610s | |
sys 0m0.008s | |
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) | |
real 3m22.465s | |
user 3m22.457s | |
sys 0m0.000s | |
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) | |
real 2m8.539s | |
user 2m8.531s | |
sys 0m0.004s | |
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' 14'' | |
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. 23' 47'' | |
frodock> | |
real 23m47.288s | |
user 23m47.183s | |
sys 0m0.052s | |
STAGE-6 Clustering and visualization of predictions | |
Sort process... | |
Maximum correlation: 2166.626709 | |
Clustering process... | |
real 0m0.816s | |
user 0m0.815s | |
sys 0m0.000s | |
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 1908.425 | |
5 157.72 107.91 72.99 11.36 0.83 53.42 1853.227 | |
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 1833.717 | |
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 1826.979 | |
10 336.83 117.52 84.76 5.36 10.83 51.42 1817.084 | |
real 0m0.001s | |
user 0m0.000s | |
sys 0m0.001s | |
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 1908.425 => 3hfl_ly2_4.pdb | |
5 157.72 107.91 72.99 11.36 0.83 53.42 1853.227 => 3hfl_ly2_5.pdb | |
real 0m0.015s | |
user 0m0.017s | |
sys 0m0.000s | |
TEST FINISHED! | |
First solution (3hfl_ly2_1.pdb) should match the native structure: 3hfl_ly_ref.pdb |
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