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1 * ...
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2 * ...
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3 * Copyright (c) 1986, 1987, 1988, 1989, 1990, 1991, 1992
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4 * Molecular Simulations Incorporated
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5 * Confidential and Proprietary: All Rights Reserved
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6 * ...
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7 * ....
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8 * TEMPLATE FOR CREATING CHARMm RTF file
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9 * ....
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10 * (%_m) replaced by first 4 characters of molecule name
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11 * in QUANTA (if used)
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12 * ..
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13 * Build RTF for %m
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14 * ...
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15 * sorted alphabetically; metals follow organics
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16 * Atom type numbers 201-229 are reserved for special QUANTA display atom types.
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17 * Last current active number is 234.
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18 *
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19 22 0
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20 MASS 7 B 10.81 B ! Boron
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21 MASS 14 C 12.01100 C ! Carbonyl or Guanidinium carbon (RBT::SP2)
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22 MASS 190 C3 12.01100 C ! Carbonyl carbon in 3-membered aliphatic ring (RBT::SP2)
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23 MASS 192 C4 12.01100 C ! Carbonyl carbons in 4-membered aliphatic ring (RBT::SP2)
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24 MASS 21 C5R 12.01100 C ! Aromatic carbon in a five membered ring (RBT::SP2)
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25 MASS 23 C5RE 13.01900 C ! Extended aromatic carbon in five membered ring (RBT::SP2)
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26 MASS 28 C5RP 12.01100 C ! for Aryl-Aryl bond between C5R rings (RBT::SP2)
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27 MASS 189 C5RQ 12.01100 C ! for second Ar-Ar bond between C5RP rings (ortho) (RBT::SP2)
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28 MASS 22 C6R 12.01100 C ! Aromatic carbon in a six membered ring (RBT::SP2)
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29 MASS 24 C6RE 13.01900 C ! Extended aromatic carbon in six membered ring (RBT::SP2)
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30 MASS 29 C6RP 12.01100 C ! for Aryl-Aryl bond between C6R rings (RBT::SP2)
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31 MASS 194 C6RQ 12.01100 C ! Carbon of C6RP type ortho to C6RP pair (RBT::SP2)
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32 MASS 230 CF1 12.01100 C ! Carbon with one Fluorine (RBT::SP3)
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33 MASS 231 CF2 12.01100 C ! Carbon with two Fluorines (RBT::SP3)
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34 MASS 232 CF3 12.01100 C ! Carbons with three Fluorines (RBT::SP3)
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35 MASS 11 CH1E 13.01900 C ! Extended atom carbon with one hydrogen (RBT::SP3)
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36 MASS 12 CH2E 14.02700 C ! Extended atom carbon with two hydrogens (RBT::SP3)
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37 MASS 13 CH3E 15.03500 C ! Extended atom carbon with three hydrogens (RBT::SP3)
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38 MASS 15 CM 12.01100 C ! Carbonmonoxide, or other triply bonded, carbon (RBT::SP)
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39 MASS 199 CP3 12.01100 C ! Carbon on nitrogen in proline ring (RBT::SP3)
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40 MASS 197 CPH1 12.01100 C ! CG and CD2 carbons in histidine ring (RBT::SP2)
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41 MASS 198 CPH2 12.01100 C ! CE1 carbon in histidine ring (RBT::SP2)
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42 MASS 195 CQ66 12.01100 C ! Third adjacent pair of CR66 types in fused rings (RBT::SP2)
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43 MASS 25 CR55 12.01100 C ! Aromatic carbon-merged five membered rings (RBT::SP2)
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44 MASS 26 CR56 12.01100 C ! Aromatic carbon-merged five/six membered rings (RBT::SP2)
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45 MASS 27 CR66 12.01100 C ! Aromatic carbon-merged six membered rings (RBT::SP2)
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46 MASS 196 CS66 12.01100 C ! Second adjacent pair of CR66 types in fused rings (RBT::SP2)
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47 MASS 10 CT 12.01100 C ! Aliphatic carbon (tetrahedral) (RBT::SP3)
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48 MASS 191 CT3 12.01100 C ! in 3-membered aliphatic ring, usually tetrahedral (RBT::SP3)
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49 MASS 193 CT4 12.01100 C ! in 4-membered aliphatic ring, usually tetrahedral (RBT::SP3)
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50 MASS 16 CUA1 12.01100 C ! Carbon in double bond, first pair (RBT::SP2)
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51 MASS 17 CUA2 12.01100 C ! Carbon in double bond, second conjugated pair (RBT::SP2)
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52 MASS 20 CUA3 12.01100 C ! Carbon in double bond, third conjugated pair (RBT::SP2)
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53 MASS 18 CUY1 12.01100 C ! Carbon in triple bond, first pair (RBT::SP)
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54 MASS 19 CUY2 12.01100 C ! Carbon in triple bond, second conjugated pair (RBT::SP)
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55 MASS 1 H 1.00800 H ! Hydrogen bonding hydrogen (neutral group) (RBT::SP3)
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56 MASS 3 HA 1.00800 H ! Aliphatic or aromatic hydrogen (RBT::SP3)
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57 MASS 2 HC 1.00800 H ! Hydrogen bonding hydrogen (charged group) (RBT::SP3)
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58 MASS 9 HMU 1.00800 H ! Mu-bonded hydrogen for metals and boron-hydride (RBT::SP3)
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59 MASS 8 HO 1.00800 H ! Hydrogen on an alcohol oxygen (RBT::SP3)
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60 MASS 4 HT 1.00800 H ! TIPS3P water model hydrogen (RBT::SP3)
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61 MASS 31 N 14.00670 N ! Nitrogen; planar-valence of 3, i.e. nitrile, etc. (RBT::TRI)
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62 MASS 234 N3 14.00670 N ! Nitrogen in a three membered ring (RBT::SP3)
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63 MASS 34 N5R 14.00670 N ! Nitrogen in a five membered aromatic ring (RBT::TRI)
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64 MASS 30 N5RP 14.00670 N ! for Ar-Ar bond between five membered rings (RBT::TRI)
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65 MASS 35 N6R 14.00670 N ! Nitrogen in a six membered aromatic ring (RBT::SP2)
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66 MASS 39 N6RP 14.00670 N ! for Aryl-Aryl bond between six membered rings (RBT::SP2)
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67 MASS 37 NC 14.00670 N ! Charged guanidinium-type nitrogen (RBT::TRI)
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68 MASS 186 NC2 14.00670 N ! for neutral guanidinium group - Arg sidechain (RBT::SP2)
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69 MASS 38 NO2 14.00670 N ! Nitrogen in nitro, or related, group (RBT::TRI)
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70 MASS 32 NP 14.00670 N ! Nitrogen in peptide, amide, or related, group (RBT::TRI)
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71 MASS 183 NR1 14.00670 N ! Protonated nitrogen in neutral histidine ring (RBT::TRI)
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72 MASS 184 NR2 14.00670 N ! Unprotonated nitrogen in neutral histidine ring (RBT::SP2)
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73 MASS 185 NR3 14.00670 N ! Nitrogens in charged histidine ring (RBT::SP2)
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74 MASS 182 NR55 14.00670 N ! N at fused bond between two 5-membered aromatics (RBT::SP2)
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75 MASS 180 NR56 14.00670 N ! N at fused bond between 5 and 6-membered aryls (RBT::SP2)
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76 MASS 181 NR66 14.00670 N ! N at fused bond between two 6-membered aromatics (RBT::SP2)
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77 MASS 36 NT 14.00670 N ! Nitrogen (tetrahedral), i.e. Amine, etc. (RBT::SP3)
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78 MASS 33 NX 14.00670 N ! Proline nitrogen, or similar (RBT::TRI)
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79 MASS 40 O 15.99940 O ! Carbonyl oxygen for amides, or related structures (RBT::SP2)
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80 MASS 56 O2M 15.99940 O ! Oxygen in Si-O-Al or Al-O-Al bond (RBT::SP3)
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81 MASS 52 O5R 15.99940 O ! Oxygen in 5 membered aromatic ring-radicals, etc. (RBT::SP3)
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82 MASS 53 O6R 15.99940 O ! Oxygen in 6 membered aromatic ring-radicals, etc. (RBT::SP3)
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83 MASS 41 OA 15.99940 O ! Carbonyl oxygen for aldehydes, or related (RBT::SP2)
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84 MASS 51 OAC 15.99940 O ! Carbonyl oxygen for acids, or related (RBT::SP2)
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85 MASS 43 OC 15.99940 O ! Charged oxygen (RBT::SP3)
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86 MASS 50 OE 15.99940 O ! Ether oxygen / Acetal oxygen (RBT::SP3)
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87 MASS 47 OH2 15.99940 O ! ST2 water model oxygen (RBT::SP3)
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88 MASS 42 OK 15.99940 O ! Carbonyl oxygen for ketones, or related (RBT::SP2)
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89 MASS 48 OM 15.99940 O ! Carbonmonoxide, or other triply bonded, oxygen
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90 MASS 49 OS 15.99940 O ! Ester oxygen (RBT::TRI)
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91 MASS 57 OSH 0.00000 O ! Massless O for zeolites, or related cage cmpds.
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92 MASS 55 OSI 15.99940 O ! Oxygen in Si-O-Si bond (RBT::SP3)
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93 MASS 45 OT 15.99940 O ! Hydroxyl oxygen (tetrahedral) or Ionizable acid (RBT::SP3)
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94 MASS 46 OW 15.99940 O ! TIP3P water model oxygen (RBT::SP3)
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95 MASS 64 P6R 30.9738 P ! Phosphorous in aromatic 6-membered ring (RBT::SP3)
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96 MASS 61 PO3 30.9738 P ! Phosphorous bonded to three oxygens (RBT::SP2)
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97 MASS 62 PO4 30.9738 P ! Phosphorous bonded to four oxygens (RBT::SP2)
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98 MASS 60 PT 30.9738 P ! Phosphorous, general; usually tetrahedral (RBT::SP3)
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99 MASS 63 PUA1 30.9738 P ! Phosphorous double bond
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100 MASS 233 PUY1 30.9738 P ! Triple bonded phosphorus
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101 MASS 72 S5R 32.0600 S ! Sulphur in a five membered aromatic ring (RBT::SP3)
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102 MASS 73 S6R 32.0600 S ! Sulphur in a six membered aromatic ring (RBT::SP3)
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103 MASS 74 SE 32.060 S ! Thioether sulphur (RBT::SP3)
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104 MASS 71 SH1E 33.06800 S ! Extended atom sulphur with one hydrogen (RBT::SP3)
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105 MASS 75 SK 32.060 S ! Thioketone sulphur (RBT::SP2)
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106 MASS 76 SO1 32.0600 S ! Sulphur bonded to one oxygen (RBT::SP3)
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107 MASS 77 SO2 32.0600 S ! Sulphur bonded to two oxygens (RBT::SP3)
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108 MASS 78 SO3 32.0600 S ! Sulphur bonded to three oxygens (RBT::SP2)
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109 MASS 79 SO4 32.0600 S ! Sulphur bonded to four oxygens (RBT::SP2)
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110 MASS 70 ST 32.06000 S ! Sulphur, general; usually tetrahedral (RBT::SP3)
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111 MASS 94 XBR 79.904 Br ! Bromine
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112 MASS 93 XCL 35.45300 Cl ! Chlorine
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113 MASS 92 XF 18.99840 F ! Fluorine
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114 MASS 95 XI 126.9045 I ! Iodine
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115 MASS 91 MAL 26.9815 Al ! ALuminum
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116 MASS 6 MBE 9.01218 Be ! Beryllium
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117 MASS 84 MCA 40.080 Ca ! Calcium
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118 MASS 83 MK 39.098 K ! Potassium
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119 MASS 80 MLI 6.941 Li ! Lithium
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120 MASS 82 MMG 24.305 Mg ! Magnesium
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121 MASS 81 MNA 22.9898 Na ! Sodium
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122 MASS 90 MSI 28.0855 Si ! Silicon
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123 MASS 177 MSIU 28.08550 Si ! Silicon when as double bond
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124 MASS 86 MFE 55.85 Fe ! Iron
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125 MASS 87 MZN 65.3800 Zn ! Zinc (Added DM 30/7/2001)
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126
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127 * 4 Jan 1999 (DM) Added old types from
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128 * /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.pro
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129 * just to keep rbscore happy. The numeric force field types are ficticious
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130 * and will not be recognised by Charmm
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131 MASS 301 CX 12.011 C ! (RBT::SP2)
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132 MASS 302 CW 12.011 C ! (RBT::SP2)
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133 MASS 303 CN 12.011 C ! (RBT::SP2)
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134 MASS 304 CA 12.011 C ! (RBT::SP2)
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135 MASS 305 CB 12.011 C ! (RBT::SP2)
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136 MASS 306 CC 12.011 C ! (RBT::SP2)
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137 MASS 307 CV 12.011 C ! (RBT::SP2)
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138 MASS 308 CR 12.011 C ! (RBT::SP2)
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139 MASS 309 CP 12.011 C ! Proline carbon CG,CD (RBT::SP3)
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140 MASS 310 NA 14.007 N ! (RBT::TRI)
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141 MASS 311 NB 14.007 N ! (RBT::TRI)
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142 MASS 312 NH1 14.007 N ! (RBT::TRI)
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143 MASS 313 NH2 14.007 N ! (RBT::TRI)
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144 MASS 314 NH3 14.007 N ! (RBT::SP3)
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145 MASS 315 OH 15.999 O ! (RBT::SP3)
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146 MASS 316 S 32.060 S ! (RBT::SP3)
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147
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148 * 4 Jan 1999 (DM) Added old types from
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149 * /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.dna
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150 * just to keep rbscore happy. The numeric force field types are ficticious
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151 * and will not be recognised by Charmm
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152 MASS 400 H2 1.00800 H ! (RBT::SP3)
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153 MASS 401 CH 12.01100 C ! (RBT::SP3)
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154 MASS 402 C2 12.01100 C ! (RBT::SP3)
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155 MASS 403 CE 12.01100 C ! (RBT::SP2)
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156 MASS 404 CF 12.01100 C ! (RBT::SP2)
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157 MASS 405 CS 12.01100 C ! (RBT::SP2)
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158 MASS 406 N2 14.00670 N ! (RBT::TRI) Corrected DM 23/8/1999
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159 MASS 407 NS 14.00670 N ! (RBT::TRI)
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160 MASS 408 NH2E 16.02270 N ! (RBT::SP3)
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161 MASS 409 O2 15.99940 O ! (RBT::SP3)
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162 MASS 411 SD 22.98980 Na !
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163 MASS 412 P 30.97400 P ! (RBT::SP3)
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164 MASS 413 BR 79.90400 Br !
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165 MASS 414 MG 24.30500 Mg !
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166
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167 * 8 Jun 1999 (DM) Added types to keep wtTARrbt158.psf happy
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168 MASS 450 HE 1.00800 H ! (RBT::SP3)
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169
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170 * 18 Jan 2001 (DM) Dummy atom type
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171 MASS 666 DUM 0.00000 DU ! Dummy atom
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172
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173 * Charmm 27 additions
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174 MASS 5 H 1.00800 H ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3)
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175 MASS 54 HG 1.00800 H ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3)
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176 MASS 58 NE 14.00670 N ! charmm27 N
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177
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178 RESI XXXX 0.0
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179
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180 END
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