Hi all,
I am trying to dock a ligand to a protein with LigandFit. I get 68 poses however with out clustering. I did set the parameter of clustering ON, however, I still could not get it. Any suggestion? Thanks in advance. Below is the content of my log file:
Read docking and energy parameter file: LF_param.txt
Read site data file: BindingSite.txt
Site partition: 1 site partition(s) produced
Site partition(s) from site data file: 1
Prepare dreiding grid, size: 57 50 47
Grid calculation finished in 31.0[s]
Site fusing: 1 fused site partition(s) produced
Monte Carlo Docking Parameters:
TORSION ITERATIONS STOP_STEPS
(1) 2 500 120
(2) 4 1200 300
(3) 6 1500 350
(4) 10 2000 500
(5) 25 3000 750
(6) 28 3500 2000
(7) 100 0 0
----------------------------------------
Molecule: B12_1N4A
Molecule no. : 1
Rotatable bonds: 28
MC termination values: 98000 / 56000
Flexible Docking ... done 604.8[s]
Clustering 100 poses...done 0.03[s] See here, DS did clustering, but where can I get it?
Molecule Pose Score dPMI
1 1 106.99 0.59
1 2 -37.62 4.68
1 3 -58.88 4.06
1 4 -100.57 1.00
1 5 -35.21 3.02
1 6 -23.75 4.54
1 7 -18.28 3.78
1 8 -84.53 4.17
1 9 -98.34 4.98
1 10 -20.31 4.41
1 11 4.49 1.41
1 12 -98.85 3.88
1 13 -60.86 2.31
1 14 21.10 3.60
1 15 3.69 4.98
1 16 -68.87 5.03
1 17 -86.62 5.07
1 18 -84.49 2.31
1 19 -35.33 0.42
1 20 -96.15 2.31
1 21 -11.62 1.37
1 22 -17.58 1.37
1 23 -88.41 2.01
1 24 102.41 2.92
1 25 -78.75 4.49
1 26 -3.86 2.70
1 27 -32.26 3.60
1 28 65.55 2.39
1 29 -64.14 3.02
1 30 -86.97 3.50
1 31 -73.30 1.91
1 32 -36.11 4.10
1 33 -84.03 1.61
1 34 22.81 3.59
1 35 -7.38 4.10
1 36 -67.09 3.73
1 37 -90.42 2.01
1 38 -74.11 4.85
1 39 8.51 3.78
1 40 -86.30 4.85
1 41 -102.51 1.91
1 42 -15.48 4.68
1 43 -16.35 3.78
1 44 1.27 3.60
1 45 -97.54 1.68
1 46 -73.27 4.28
1 47 -54.09 1.92
1 48 18.94 4.41
1 49 -101.65 1.99
1 50 105.49 3.60
1 51 40.82 4.36
1 52 -96.07 4.23
1 53 -89.45 4.65
1 54 -74.32 4.47
1 55 -25.61 4.92
1 56 -9.53 4.92
1 57 -12.14 5.50
1 58 -100.02 5.20
1 59 -45.65 3.59
1 60 -18.52 3.03
1 61 -87.37 0.42
1 62 106.74 2.73
1 63 -5.92 2.21
1 64 115.37 5.07
1 65 -79.65 5.71
1 66 -45.60 5.27
1 67 111.26 2.73
1 68 -24.63 5.27
----------------------------------------
Poses saved: 68
Total elapsed time: 10:37 [min:sec]
Run completed at: Wed Jul 29 17:15:31 2009
Released license for ligfit_ext...
I am trying to dock a ligand to a protein with LigandFit. I get 68 poses however with out clustering. I did set the parameter of clustering ON, however, I still could not get it. Any suggestion? Thanks in advance. Below is the content of my log file:
Read docking and energy parameter file: LF_param.txt
Read site data file: BindingSite.txt
Site partition: 1 site partition(s) produced
Site partition(s) from site data file: 1
Prepare dreiding grid, size: 57 50 47
Grid calculation finished in 31.0[s]
Site fusing: 1 fused site partition(s) produced
Monte Carlo Docking Parameters:
TORSION ITERATIONS STOP_STEPS
(1) 2 500 120
(2) 4 1200 300
(3) 6 1500 350
(4) 10 2000 500
(5) 25 3000 750
(6) 28 3500 2000
(7) 100 0 0
----------------------------------------
Molecule: B12_1N4A
Molecule no. : 1
Rotatable bonds: 28
MC termination values: 98000 / 56000
Flexible Docking ... done 604.8[s]
Clustering 100 poses...done 0.03[s] See here, DS did clustering, but where can I get it?
Molecule Pose Score dPMI
1 1 106.99 0.59
1 2 -37.62 4.68
1 3 -58.88 4.06
1 4 -100.57 1.00
1 5 -35.21 3.02
1 6 -23.75 4.54
1 7 -18.28 3.78
1 8 -84.53 4.17
1 9 -98.34 4.98
1 10 -20.31 4.41
1 11 4.49 1.41
1 12 -98.85 3.88
1 13 -60.86 2.31
1 14 21.10 3.60
1 15 3.69 4.98
1 16 -68.87 5.03
1 17 -86.62 5.07
1 18 -84.49 2.31
1 19 -35.33 0.42
1 20 -96.15 2.31
1 21 -11.62 1.37
1 22 -17.58 1.37
1 23 -88.41 2.01
1 24 102.41 2.92
1 25 -78.75 4.49
1 26 -3.86 2.70
1 27 -32.26 3.60
1 28 65.55 2.39
1 29 -64.14 3.02
1 30 -86.97 3.50
1 31 -73.30 1.91
1 32 -36.11 4.10
1 33 -84.03 1.61
1 34 22.81 3.59
1 35 -7.38 4.10
1 36 -67.09 3.73
1 37 -90.42 2.01
1 38 -74.11 4.85
1 39 8.51 3.78
1 40 -86.30 4.85
1 41 -102.51 1.91
1 42 -15.48 4.68
1 43 -16.35 3.78
1 44 1.27 3.60
1 45 -97.54 1.68
1 46 -73.27 4.28
1 47 -54.09 1.92
1 48 18.94 4.41
1 49 -101.65 1.99
1 50 105.49 3.60
1 51 40.82 4.36
1 52 -96.07 4.23
1 53 -89.45 4.65
1 54 -74.32 4.47
1 55 -25.61 4.92
1 56 -9.53 4.92
1 57 -12.14 5.50
1 58 -100.02 5.20
1 59 -45.65 3.59
1 60 -18.52 3.03
1 61 -87.37 0.42
1 62 106.74 2.73
1 63 -5.92 2.21
1 64 115.37 5.07
1 65 -79.65 5.71
1 66 -45.60 5.27
1 67 111.26 2.73
1 68 -24.63 5.27
----------------------------------------
Poses saved: 68
Total elapsed time: 10:37 [min:sec]
Run completed at: Wed Jul 29 17:15:31 2009
Released license for ligfit_ext...
