Created
January 31, 2016 16:58
-
-
Save 0x3bfc/8083a293636ee65fa17a to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 [email protected] 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 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment