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January 31, 2016 16:58
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| ubuntu@ip-172-31-5-104:~/frodock/FRODOCK_v2.0_Linux$ time ./run_frodock_tests.sh 1a8m 1alu 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... | |
| ssh -i /home/ahmed/Dropbox/EHPC-Container-results/keys/cudakey.pem ubuntu@52.53.236.135ASA 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 | |
| WARNING reading 1alu.pdb : Alt-loc[61 CB ] Alt-loc[63 CG ] Alt-loc[65 OD1] Alt-loc[67 OD2] Alt-loc[99 CB ] Alt-loc[101 CG ] Alt-loc[103 CD ] Alt-loc[105 NE ] Alt-loc[107 CZ ] Alt-loc[109 NH1] Alt-loc[111 NH2] Alt-loc[723 CB ] Alt-loc[725 CG ] Alt-loc[727 SD ] Alt-loc[729 CE ] | |
| 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 1398 atoms... | |
| ASA pdb file 1alu_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: 475326 (skipped: 254763 out: 1009410) | |
| 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: 2.410470 -20.282412 8.860263 | |
| 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: 29.448612 (30 spherical layers) | |
| frodock> Receptor max radius in A 42.657120 81.314240 | |
| frodock> Ligand electrostatic radius in A: 29.448612 (30 spherical layers) | |
| frodock> Ligand accessibility radius in A: 29.448612 (30 spherical layers) | |
| frodock> Ligand desolvation radius in A: 34.448612 (35 spherical layers) | |
| frodock> Maximum ligand desolvation radius in A: 34.448612 (35 spherical layers) | |
| frodock> Precomputation of Ligand spherical representation Time: 00h. 00' 18'' | |
| frodock> | |
| frodock> Determination of translational points to explore | |
| adp_pp> Maximum size of the PDB(in amstrongs): 29.000000 | |
| adp_pp> Minimum size of the PDB:(in amstrongs) 11.000000 | |
| dilateMax=21.000000 voxel_lig_out[1]=29.000000 limitMaxMask=0.250000 | |
| dilateMin=8.000000 voxel_lig_out[0]=11.000000 limitMinMask=0.260000 | |
| vol final: 103 103 100 | |
| radiusMax_lig_amstrongs_backbone=30.448612frodock> Mask created | |
| frodock> Number of points to explore: 39608 saving all best solutions | |
| frodock> | |
| frodock> Searching 100.00 | |
| frodock> Number of solutions: 121936 | |
| frodock> Total time: 01h. 18' 13'' | |
| frodock> | |
| STAGE-6 Clustering and visualization of predictions | |
| WARNING reading 1alu.pdb : Alt-loc[61 CB ] Alt-loc[63 CG ] Alt-loc[65 OD1] Alt-loc[67 OD2] Alt-loc[99 CB ] Alt-loc[101 CG ] Alt-loc[103 CD ] Alt-loc[105 NE ] Alt-loc[107 CZ ] Alt-loc[109 NH1] Alt-loc[111 NH2] Alt-loc[723 CB ] Alt-loc[725 CG ] Alt-loc[727 SD ] Alt-loc[729 CE ] | |
| Sort process... | |
| Maximum correlation: 1496.144775 | |
| Clustering process... | |
| STAGE-7 Visualize the first 10 solutions | |
| 1 313.35 69.29 159.41 -7.43 30.35 20.28 1496.145 | |
| 2 41.40 130.41 11.05 8.57 68.35 68.28 1456.878 | |
| 3 198.90 60.10 107.14 8.57 70.35 64.28 1405.633 | |
| 4 253.87 60.43 291.30 -5.43 28.35 30.28 1389.711 | |
| 5 92.80 13.80 25.28 16.57 68.35 72.28 1363.220 | |
| 6 76.55 34.76 296.82 34.57 74.35 20.28 1361.203 | |
| 7 236.10 121.16 152.88 44.57 66.35 18.28 1353.969 | |
| 8 203.59 86.31 7.63 26.57 68.35 80.28 1344.516 | |
| 9 26.96 84.89 164.81 14.57 72.35 64.28 1334.625 | |
| 10 155.95 100.57 77.61 -5.43 18.35 28.28 1329.138 | |
| STAGE-8 Coordinate generation of the 5 best predicted solutions | |
| WARNING reading 1alu.pdb : Alt-loc[61 CB ] Alt-loc[63 CG ] Alt-loc[65 OD1] Alt-loc[67 OD2] Alt-loc[99 CB ] Alt-loc[101 CG ] Alt-loc[103 CD ] Alt-loc[105 NE ] Alt-loc[107 CZ ] Alt-loc[109 NH1] Alt-loc[111 NH2] Alt-loc[723 CB ] Alt-loc[725 CG ] Alt-loc[727 SD ] Alt-loc[729 CE ] | |
| 1 313.35 69.29 159.41 -7.43 30.35 20.28 1496.145 => 1alu_1.pdb | |
| 2 41.40 130.41 11.05 8.57 68.35 68.28 1456.878 => 1alu_2.pdb | |
| 3 198.90 60.10 107.14 8.57 70.35 64.28 1405.633 => 1alu_3.pdb | |
| 4 253.87 60.43 291.30 -5.43 28.35 30.28 1389.711 => 1alu_4.pdb | |
| 5 92.80 13.80 25.28 16.57 68.35 72.28 1363.220 => 1alu_5.pdb | |
| TEST FINISHED! | |
| First solution (1alu_1.pdb) should match the native structure: 3hfl_ly_ref.pdb | |
| real 87m51.216s | |
| user 87m35.744s | |
| sys 0m0.594s |
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