1########################################################################## 2### PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE 3### $Id$ 4### 5### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for 6### syntax help. 7########################################################################## 8 9read 10 mol pqr bx6_7_lig_apbs.pqr 11 mol pqr bx6_7_apo_apbs.pqr 12 mol pqr bx6_7_bin_apbs.pqr 13end 14 15# LIGAND ENERGY (FOCUSING) 16elec name lig-coarse 17 mg-manual 18 dime 97 97 97 19 glen 70 70 70 20 gcent mol 3 21 mol 1 22 lpbe 23 bcfl sdh 24 ion charge 1 conc 0.000 radius 2.0 25 ion charge -1 conc 0.000 radius 2.0 26 pdie 2.0 27 sdie 78.00 28 chgm spl0 29 srfm smol 30 srad 0.0 31 swin 0.3 32 sdens 10.0 33 temp 298.15 34 calcenergy total 35 calcforce no 36end 37elec name lig-fine 38 mg-manual 39 dime 97 97 97 40 grid 0.25 0.25 0.25 41 gcent mol 1 42 mol 1 43 lpbe 44 bcfl focus 45 ion charge 1 conc 0.000 radius 2.0 46 ion charge -1 conc 0.000 radius 2.0 47 pdie 2.0 48 sdie 78.00 49 chgm spl0 50 srfm smol 51 srad 0.0 52 swin 0.3 53 sdens 10.0 54 temp 298.15 55 calcenergy total 56 calcforce no 57end 58 59# KINASE ENERGY (FOCUSING) 60elec name pka-coarse 61 mg-manual 62 dime 97 97 97 63 glen 70 70 70 64 gcent mol 3 65 mol 2 66 lpbe 67 bcfl sdh 68 ion charge 1 conc 0.000 radius 2.0 69 ion charge -1 conc 0.000 radius 2.0 70 pdie 2.0 71 sdie 78.00 72 chgm spl0 73 srfm smol 74 srad 0.0 75 swin 0.3 76 sdens 10.0 77 temp 298.15 78 calcenergy total 79 calcforce no 80end 81elec name pka-fine 82 mg-manual 83 dime 97 97 97 84 grid 0.25 0.25 0.25 85 gcent mol 1 86 mol 2 87 lpbe 88 bcfl focus 89 ion charge 1 conc 0.000 radius 2.0 90 ion charge -1 conc 0.000 radius 2.0 91 pdie 2.0 92 sdie 78.00 93 chgm spl0 94 srfm smol 95 srad 0.0 96 swin 0.3 97 sdens 10.0 98 temp 298.15 99 calcenergy total 100 calcforce no 101end 102 103# COMPLEX ENERGY (FOCUSING) 104elec name complex-coarse 105 mg-manual 106 dime 97 97 97 107 glen 70 70 70 108 gcent mol 3 109 mol 3 110 lpbe 111 bcfl sdh 112 ion charge 1 conc 0.000 radius 2.0 113 ion charge -1 conc 0.000 radius 2.0 114 pdie 2.0 115 sdie 78.00 116 chgm spl0 117 srfm smol 118 srad 0.0 119 swin 0.3 120 sdens 10.0 121 temp 298.15 122 calcenergy total 123 calcforce no 124end 125elec name complex-fine 126 mg-manual 127 dime 97 97 97 128 grid 0.25 0.25 0.25 129 gcent mol 1 130 mol 3 131 lpbe 132 bcfl focus 133 ion charge 1 conc 0.000 radius 2.0 134 ion charge -1 conc 0.000 radius 2.0 135 pdie 2.0 136 sdie 78.00 137 chgm spl0 138 srfm smol 139 srad 0.0 140 swin 0.3 141 sdens 10.0 142 temp 298.15 143 calcenergy total 144 calcforce no 145end 146 147print elecEnergy complex-fine - lig-fine - pka-fine end 148 149quit 150