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annotate tools/rdock/data/sf/RbtInterIdxSF.prm @ 5:a2f9c8a46a4b draft default tip

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author marpiech
date Thu, 06 Oct 2016 07:09:26 -0400
parents 75f2b4087722
children
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1 RBT_PARAMETER_FILE_V1.00
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2 TITLE Intermolecular scoring function (without SOLVATION, indexed VDW)
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3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterIdxSF.prm#3 $
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4
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5 ################################################################################
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6 # Constant scoring function
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7 # Represents loss of translation, rotational entropy of ligand
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8 # DM 14 June 2006 - also calculates solvent penalty for all enabled solvent
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9 # SOLVENT_PENALTY is defined as a fraction of the ligand binding penalty
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10 # i.e. ligand binding penalty = 1.0 * WEIGHT
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11 # solvent binding penalty = N(enabled solvent) * SOLVENT_PENALTY * WEIGHT
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12 # 0.37 * 5.4 = 2.0 kJ/mol, which corresponds to GOLD Chemscore penalty
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13 # Verdonk et al, J. Med. Chem. 2005 (48) 6504-6515
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14 SECTION CONST
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15 SCORING_FUNCTION RbtConstSF
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16 SOLVENT_PENALTY 0.37
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17 WEIGHT +5.4
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18 END_SECTION
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19
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20 ################################################################################
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21 # Rotational scoring function
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22 # Represents loss of torsional entropy of ligand
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23 SECTION ROT
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24 SCORING_FUNCTION RbtRotSF
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25 WEIGHT +1.0
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26 END_SECTION
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27
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28 ################################################################################
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29 # Pseudo SFs for setting up atomic attributes for polar and lipo atoms
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30 SECTION SETUP_POLAR
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31 SCORING_FUNCTION RbtSetupPolarSF
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32 RADIUS 5.0
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33 NORM 25
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34 POWER 0.5
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35 CHGFACTOR 0.5
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36 GUANFACTOR 0.5
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37 END_SECTION
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38
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39 ################################################################################
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40 # Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
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41 SECTION POLAR
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42 SCORING_FUNCTION RbtPolarIdxSF
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43 WEIGHT 3.4
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44 R12FACTOR 1.0
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45 R12INCR 0.05
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46 DR12MIN 0.25
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47 DR12MAX 0.6
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48 A1 180.0
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49 DA1MIN 30.0
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50 DA1MAX 80.0
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51 A2 180.0
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52 DA2MIN 60.0
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53 DA2MAX 100.0
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54 INCMETAL TRUE
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55 INCHBD TRUE
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56 INCHBA TRUE
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57 INCGUAN TRUE
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58 GUAN_PLANE TRUE
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59 ABS_DR12 TRUE
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60 GRIDSTEP 0.5
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61 RANGE 5.31
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62 INCR 3.36
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63 ATTR TRUE
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64 LP_OSP2 TRUE
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65 LP_PHI 45
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66 LP_DPHIMIN 15
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67 LP_DPHIMAX 30
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68 LP_DTHETAMIN 20
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69 LP_DTHETAMAX 60
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70 END_SECTION
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71
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72 ################################################################################
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73 # Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc)
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74 SECTION REPUL
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75 SCORING_FUNCTION RbtPolarIdxSF
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76 WEIGHT 5.0
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77 R12FACTOR 1.0
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78 R12INCR 0.6
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79 DR12MIN 0.25
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80 DR12MAX 1.1
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81 A1 180.0
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82 DA1MIN 30.0
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83 DA1MAX 60.0
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84 A2 180.0
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85 DA2MIN 30.0
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86 DA2MAX 60.0
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87 INCMETAL TRUE
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88 INCHBD TRUE
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89 INCHBA TRUE
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90 INCGUAN TRUE
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91 GUAN_PLANE FALSE
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92 ABS_DR12 FALSE
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93 GRIDSTEP 0.5
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94 RANGE 5.32
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95 INCR 3.51
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96 ATTR FALSE
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97 LP_OSP2 FALSE
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98 END_SECTION
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99
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100 ################################################################################
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101 # Aromatic (pi-pi) scoring function, also used for cation-pi
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102 #SECTION AROM
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103 # SCORING_FUNCTION RbtAromIdxSF
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104 # WEIGHT -1.8
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105 # R12 3.5
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106 # DR12MIN 0.25
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107 # DR12MAX 0.6
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108 # DAMIN 20.0
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109 # DAMAX 30.0
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110 # GRIDSTEP 0.5
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111 # RANGE 4.1
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112 # INCR 4.1
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113 #END_SECTION
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114
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115 ################################################################################
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116 # Van der Waals scoring function
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117 SECTION VDW
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118 SCORING_FUNCTION RbtVdwIdxSF
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119 WEIGHT 1.0
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120 USE_4_8 FALSE
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121 USE_TRIPOS FALSE
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122 RMAX 1.5
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123 ECUT 120.0
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124 E0 1.5
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125 FAST_SOLVENT TRUE
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126 END_SECTION