1 | ! *******************************************************************
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2 | ! SMMP version of Anders Irback's force field, to be called the Lund
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3 | ! force field. This file contains the function enylun, which in turn
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4 | ! calls all the terms in the energy function. The terms Bias (ebias),
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5 | ! Hydrogen bonds (ehbmm and ehbms), Hydrophobicity (ehp) and the
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6 | ! Excluded volume (eexvol and eloexv) are also implemented in this
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7 | ! file.
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8 | !
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9 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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10 | ! Jan H. Meinke, Sandipan Mohanty
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11 | !
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12 | subroutine set_local_constr(ires,frst,lst,root)
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13 | include 'INCL.H'
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14 | include 'incl_lund.h'
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15 | integer ires,frst,lst,root
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16 | do iat1=iCa(ires)+frst,iCa(ires)+lst
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17 | do iat2=iat1+1,iCa(ires)+lst
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18 | matcon(iat2-iat1,iat1)=0
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19 | matcon(iat1-iat2,iat2)=0
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20 | enddo
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21 | enddo
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22 | iat1=iCa(ires)+root
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23 | do iat2=iCa(ires)+root,iCa(ires)+lst
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24 | matcon(iat2-iat1,iat1)=0
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25 | matcon(iat1-iat2,iat2)=0
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26 | enddo
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27 | end subroutine set_local_constr
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28 |
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29 | subroutine init_lundff
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30 | include 'INCL.H'
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31 | include 'incl_lund.h'
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32 | character mynm*4
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33 | logical prlvr
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34 |
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35 | print *,'initializing Lund forcefield'
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36 | ! Some parameters in the Lund force field.
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37 | ! The correspondence between internal energy scale and kcal/mol
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38 | eunit=1.3315d0
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39 | ! eunit=1.0
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40 | ! Bias
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41 | kbias=100.0d0*eunit
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42 | ! print *,'Bias'
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43 | ! Hydrogen bonds
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44 | epshb1=3.1d0*eunit
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45 | epshb2=2.0d0*eunit
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46 | sighb=2.0d0
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47 | cthb=4.5d0
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48 | cthb2=cthb*cthb
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49 | powa=0.5d0
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50 | powb=0.5d0
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51 | blhb=-30.0d0*(((sighb/cthb)**10-(sighb/cthb)**12))/cthb2
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52 | alhb=-(5*((sighb/cthb)**12)-6*((sighb/cthb)**10))-blhb*cthb2
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53 | sighb2=sighb*sighb
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54 | cdon=1.0d0
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55 | cacc=(1.0d0/1.23d0)**powb
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56 | csacc=(1.0d0/1.25d0)**powb
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57 | ! print *,'Hydrogen bonds'
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58 | ! Hydrophobicity
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59 | ! print *,'Hydrophobicity with nhptyp = ',nhptyp
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60 |
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61 | hpstrg(1)=0.0d0*eunit
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62 | hpstrg(2)=0.1d0*eunit
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63 | hpstrg(3)=0.1d0*eunit
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64 | hpstrg(4)=0.1d0*eunit
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65 | hpstrg(5)=0.9d0*eunit
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66 | hpstrg(6)=2.8d0*eunit
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67 | hpstrg(7)=0.1d0*eunit
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68 | hpstrg(8)=2.8d0*eunit
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69 | hpstrg(9)=3.2d0*eunit
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70 |
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71 | do i=1,mxrs
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72 | do j=1,6
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73 | ihpat(i,j)=0
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74 | enddo
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75 | nhpat(i)=0
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76 | enddo
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77 | do i=irsml1(1),irsml2(ntlml)
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78 | mynm=seq(i)
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79 | call tolost(mynm)
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80 | if ((mynm.eq.'pro').or.(mynm.eq.'cpro')
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81 | & .or.(mynm.eq.'cpru').or.(mynm.eq.'prou')
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82 | & .or.(mynm.eq.'pron').or.(mynm.eq.'pro+')) then
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83 | prlvr=.true. ! residue i is a proline variant
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84 | print *, 'proline variant ',mynm,i
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85 | else
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86 | prlvr=.false.
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87 | endif
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88 |
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89 | if (mynm.eq.'ala') then
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90 | nhpat(i)=1
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91 | ihpat(i,1)=iCa(i)+2
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92 | else if (mynm.eq.'val') then
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93 | nhpat(i)=3
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94 | ihpat(i,1)=iCa(i)+2
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95 | ihpat(i,2)=iCa(i)+4
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96 | ihpat(i,3)=iCa(i)+8
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97 | else if (prlvr) then
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98 | nhpat(i)=3
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99 | ihpat(i,1)=iCa(i)+2
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100 | ihpat(i,2)=iCa(i)+5
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101 | ihpat(i,3)=iCa(i)+8
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102 | else if (mynm.eq.'leu') then
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103 | nhpat(i)=4
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104 | ihpat(i,1)=iCa(i)+2
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105 | ihpat(i,2)=iCa(i)+5
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106 | ihpat(i,3)=iCa(i)+7
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107 | ihpat(i,4)=iCa(i)+11
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108 | else if (mynm.eq.'ile') then
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109 | nhpat(i)=4
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110 | ihpat(i,1)=iCa(i)+2
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111 | ihpat(i,2)=iCa(i)+4
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112 | ihpat(i,3)=iCa(i)+8
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113 | ihpat(i,4)=iCa(i)+11
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114 | else if (mynm.eq.'met') then
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115 | nhpat(i)=4
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116 | ihpat(i,1)=iCa(i)+2
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117 | ihpat(i,2)=iCa(i)+5
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118 | ihpat(i,3)=iCa(i)+8
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119 | ihpat(i,4)=iCa(i)+9
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120 | else if (mynm.eq.'phe') then
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121 | nhpat(i)=6
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122 | ihpat(i,1)=iCa(i)+5
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123 | ihpat(i,2)=iCa(i)+6
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124 | ihpat(i,3)=iCa(i)+8
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125 | ihpat(i,4)=iCa(i)+10
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126 | ihpat(i,5)=iCa(i)+12
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127 | ihpat(i,6)=iCa(i)+14
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128 | else if (mynm.eq.'tyr') then
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129 | nhpat(i)=6
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130 | ihpat(i,1)=iCa(i)+5
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131 | ihpat(i,2)=iCa(i)+6
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132 | ihpat(i,3)=iCa(i)+8
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133 | ihpat(i,4)=iCa(i)+10
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134 | ihpat(i,5)=iCa(i)+13
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135 | ihpat(i,6)=iCa(i)+15
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136 | else if (mynm.eq.'trp') then
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137 | nhpat(i)=6
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138 | ihpat(i,1)=iCa(i)+10
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139 | ihpat(i,2)=iCa(i)+11
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140 | ihpat(i,3)=iCa(i)+13
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141 | ihpat(i,4)=iCa(i)+15
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142 | ihpat(i,5)=iCa(i)+17
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143 | ihpat(i,6)=iCa(i)+19
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144 | endif
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145 | enddo
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146 | ! print *,'Hydrophobicity'
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147 |
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148 | ! Excluded volume and local pair excluded volume terms
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149 | exvk=0.1*eunit
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150 | exvcut=4.3
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151 | exvcut2=exvcut*exvcut
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152 |
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153 | sigsa(1)=1.0d0 ! hydrogen
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154 | sigsa(2)=1.0d0 ! hydrogen
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155 | sigsa(3)=1.0d0 ! hydrogen
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156 | sigsa(4)=1.0d0 ! hydrogen
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157 | sigsa(5)=1.0d0 ! hydrogen
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158 | sigsa(6)=1.0d0 ! hydrogen
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159 | sigsa(7)=1.75d0 ! carbon
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160 | sigsa(8)=1.75d0 ! carbon
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161 | sigsa(9)=1.75d0 ! carbon
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162 | sigsa(10)=1.42d0 ! oxygen
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163 | sigsa(11)=1.42d0 ! oxygen
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164 | sigsa(12)=1.42d0 ! oxygen
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165 | sigsa(13)=1.55d0 ! nitrogen
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166 | sigsa(14)=1.55d0 ! nitrogen
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167 | sigsa(15)=1.55d0 ! nitrogen
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168 | sigsa(16)=1.77d0 ! sulfur
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169 | sigsa(17)=1.0d0 ! hydrogen
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170 | sigsa(18)=1.75d0 ! carbon
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171 |
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172 | do i=1,mxtyat
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173 | do j=1,mxtyat
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174 | sig2lcp(i,j)=(sigsa(i)+sigsa(j))**2
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175 | asalcp(i,j)=-7*((sig2lcp(i,j)/exvcut2)**6.0d0)
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176 | bsalcp(i,j)=6*((sig2lcp(i,j)/exvcut2)**6.0d0)/exvcut2
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177 | enddo
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178 | enddo
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179 | ! print *,'Local pair excluded volume constants'
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180 |
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181 | exvlam=0.75d0
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182 | exvcutg=exvcut*exvlam
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183 | exvcutg2=exvcutg*exvcutg
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184 |
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185 | do i=1,mxtyat
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186 | do j=1,mxtyat
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187 | sig2exv(i,j)=(exvlam*(sigsa(i)+sigsa(j)))**2
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188 | asaexv(i,j)=-7*((sig2exv(i,j)/exvcutg2)**6.0)
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189 | bsaexv(i,j)=6*((sig2exv(i,j)/exvcutg2)**6.0)/exvcutg2
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190 | enddo
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191 | enddo
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192 | ! print *,'General excluded volume constants'
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193 |
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194 | ! Initialization of the connections matrix matcon(i,j). The index
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195 | ! i runs from -mxconr to +mxconr, and j from 1 to mxat.
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196 | ! matcon(i2-i1,i1) = 0, if the distance between atoms i1 and i2 is fixed
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197 | ! = 2, if atoms i1 and i2 are separated by 3 covalent
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198 | ! bonds and their distance can change
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199 | ! = 1, for all other pairs
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200 | ! if abs(i2-i1) > mxconr, the atoms are assumed to be separated by
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201 | ! many bonds, and with no restriction on their distances. On a protein
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202 | ! molecule made of natural amino acids, atoms with indices separated
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203 | ! by more than 35 can not be connected by three covalent bonds.
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204 |
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205 | do i=1,mxat
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206 | do j=-mxconr,mxconr
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207 | matcon(j,i)=1
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208 | enddo
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209 | matcon(0,i)=0
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210 | enddo
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211 | ! continued...
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212 | do iml=1,ntlml
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213 | do iat1=iatrs1(irsml1(iml)),iatrs2(irsml2(iml))
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214 | do j=1,nbdat(iat1)
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215 | iat2=ibdat(j,iat1)
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216 | matcon(iat2-iat1,iat1)=0 ! directly bonded atoms
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217 | matcon(iat1-iat2,iat2)=0 !
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218 | do k=1,nbdat(iat2)
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219 | iat3=ibdat(k,iat2)
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220 | matcon(iat3-iat1,iat1)=0 !
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221 | matcon(iat1-iat3,iat3)=0 ! 2 covalent bonds
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222 | do l=1,nbdat(iat3)
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223 | iat4=ibdat(l,iat3)
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224 | if (iat4.ne.iat2) then
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225 | matcon(iat4-iat1,iat1)=2 !
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226 | matcon(iat1-iat4,iat4)=2 ! 3 covalent bonds
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227 | endif
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228 | do m=1,nbdat(iat2)
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229 | iat3p=ibdat(m,iat2)
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230 | if (iat3p.ne.iat3) then
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231 | matcon(iat4-iat3p,iat3p)=2 ! 3 covalent bonds
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232 | matcon(iat3p-iat4,iat4)=2 !
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233 | endif
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234 | enddo
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235 | enddo
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236 | enddo
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237 | do k=1,nbdat(iat1)
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238 | iat3=ibdat(k,iat1)
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239 | matcon(iat3-iat2,iat2)=0 ! also 2 bonds iat2-iat1-iat3
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240 | matcon(iat2-iat3,iat3)=0 !
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241 | enddo
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242 | enddo
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243 | enddo
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244 |
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245 | ! print *,'going to initialize connections for first residue'
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246 | ! print *,'iN,iCa,iC =',iN(irsml1(iml)),
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247 | ! # iCa(irsml1(iml)),iC(irsml1(iml))
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248 | do iat1=iN(irsml1(iml))+1,iCa(irsml1(iml))-1
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249 | ! print *,'connections for iat1 = ',iat1
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250 | matcon(iat1-iN(irsml1(iml)),iN(irsml1(iml)))=0
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251 | matcon(iN(irsml1(iml))-iat1,iat1)=0
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252 | matcon(iat1-iCa(irsml1(iml)),iCa(irsml1(iml)))=0
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253 | matcon(iCa(irsml1(iml))-iat1,iat1)=0
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254 | do iat2=iat1,iCa(irsml1(iml))-1
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255 | matcon(iat2-iat1,iat1)=0
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256 | matcon(iat1-iat2,iat2)=0
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257 | enddo
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258 | matcon(iat1-iCa(irsml1(iml))-1,iCa(irsml1(iml))+1)=2
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259 | matcon(iCa(irsml1(iml))+1-iat1,iat1)=2
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260 | matcon(iat1-iCa(irsml1(iml))-2,iCa(irsml1(iml))+2)=2
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261 | matcon(iCa(irsml1(iml))+2-iat1,iat1)=2
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262 | matcon(iat1-iC(irsml1(iml)),iC(irsml1(iml)))=2
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263 | matcon(iC(irsml1(iml))-iat1,iat1)=2
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264 | enddo
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265 |
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266 | ! Below: for certain residues, some atoms separated by 3 or more bonds
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267 | ! do not change distance. So, the connection matrix term for such pairs
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268 | ! should be zero.
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269 |
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270 | do irs=irsml1(iml),irsml2(iml)
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271 | if (irs.eq.irsml1(iml)) then
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272 | iatoff=1
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273 | else
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274 | iatoff=0
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275 | endif
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276 | if (irs.eq.irsml2(iml)) then
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277 | iatmrg=2
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278 | else
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279 | iatmrg=0
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280 | endif
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281 | mynm=seq(irs)
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282 | call tolost(mynm)
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283 | if ((mynm.eq.'pro')) then
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284 | prlvr=.true. ! residue i is a proline variant
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285 | else
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286 | prlvr=.false.
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287 | endif
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288 | if ((mynm.eq.'asn')) then
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289 | call set_local_constr(irs,5,9,2)
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290 | else if ((mynm.eq.'gln')) then
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291 | call set_local_constr(irs,8,12,5)
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292 | else if ((mynm.eq.'arg')) then
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293 | call set_local_constr(irs,11,19,8)
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294 | else if ((mynm.eq.'his')) then
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295 | call set_local_constr(irs,5,12,2)
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296 | else if (mynm.eq.'phe') then
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297 | call set_local_constr(irs,5,15,2)
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298 | else if (mynm.eq.'tyr') then
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299 | call set_local_constr(irs,5,16,2)
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300 | iat1=iCa(irs)+12 ! H_h
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301 | iat2=iCa(irs)+13 ! C_e2
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302 | iat3=iCa(irs)+8 ! C_e1
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303 | matcon(iat2-iat1,iat1)=2
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304 | matcon(iat1-iat2,iat2)=2
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305 | matcon(iat3-iat1,iat1)=2
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306 | matcon(iat1-iat3,iat3)=2
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307 | else if (mynm.eq.'trp') then
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308 | call set_local_constr(irs,5,19,2)
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309 | else if (prlvr) then
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310 | ! Proline. Many more distances are fixed because of the fixed
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311 | ! phi angle
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312 | call set_local_constr(irs,-3,11,-3)
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313 | matcon(iCa(irs-1)-iCa(irs)-8,iCa(irs)+8)=0
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314 | matcon(iCa(irs)+8-iCa(irs-1),iCa(irs-1))=0
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315 | endif
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316 | enddo
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317 |
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318 | ! Distances fixed because of the constant omega angle
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319 | do irs=irsml1(iml),irsml2(iml)-1
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320 | matcon(iCa(irs+1)-iC(irs)-1,iC(irs)+1)=0 ! O_i -- Ca_{i+1}
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321 | matcon(-iCa(irs+1)+iC(irs)+1,iCa(irs+1))=0 ! O_i -- Ca_{i+1}
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322 |
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323 | matcon(iN(irs+1)-iC(irs),iC(irs)+1)=0 ! O_i -- H_{i+1}
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324 | matcon(-iN(irs+1)+iC(irs),iN(irs+1)+1)=0 ! O_i -- H_{i+1}
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325 |
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326 | matcon(iCa(irs+1)-iCa(irs),iCa(irs))=0 ! Ca_i -- Ca_{i+1}
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327 | matcon(-iCa(irs+1)+iCa(irs),iCa(irs+1))=0 ! Ca_i -- Ca_{i+1}
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328 |
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329 | matcon(iN(irs+1)+1-iCa(irs),iCa(irs))=0 ! Ca_i -- H_{i+1}
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330 | matcon(-iN(irs+1)-1+iCa(irs),iN(irs+1)+1)=0 ! Ca_i -- H_{i+1}
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331 | enddo
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332 |
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333 | enddo
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334 | ! finished initializing matrix conmat
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335 | ! print *,'Connections matrix'
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336 | ! Local pair excluded volume
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337 | do i=1,mxml
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338 | ilpst(i)=1
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339 | ilpnd(i)=0
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340 | enddo
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341 | do i=1,50*mxrs
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342 | lcp1(i)=0
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343 | lcp2(i)=0
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344 | enddo
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345 | ilp=0
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346 | do iml=1,ntlml
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347 | do iat1=iatrs1(irsml1(iml)),iatrs2(irsml2(iml))
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348 | do iat2=iat1+1,iatrs2(irsml2(iml))
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349 | if (iat2-iat1.le.mxconr) then
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350 | if (matcon(iat2-iat1,iat1).eq.2) then
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351 | ilp=ilp+1
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352 | lcp1(ilp)=iat1
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353 | lcp2(ilp)=iat2
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354 | endif
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355 | endif
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356 | enddo
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357 | enddo
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358 |
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359 | ilpnd(iml)=ilp
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360 | if (iml.lt.ntlml) then
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361 | ilpst(iml+1)=ilp+1
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362 | endif
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363 | print *,'molecule ',iml,' lc pair range ',ilpst(iml),ilpnd(iml)
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364 | ! print *,'local pair list'
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365 | do lci=ilpst(iml),ilpnd(iml)
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366 | iat1=lcp1(lci)
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367 | iat2=lcp2(lci)
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368 | ! print *,lci,iat1,iat2,ityat(iat1),ityat(iat2)
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369 | enddo
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370 | enddo
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371 | print *,'finished initializing Lund force field'
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372 | end
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373 |
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374 | integer function ihptype(iaa)
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375 | include 'INCL.H'
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376 | character mynm*4
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377 | mynm=seq(iaa)
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378 | ityp=-1
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379 | call tolost(mynm)
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380 | if (mynm.eq.'ala') then
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381 | ityp=1
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382 | else if ((mynm.eq.'val').or.(mynm.eq.'leu').or.(mynm.eq.'ile')
|
---|
383 | & .or.(mynm.eq.'met').or.(mynm.eq.'pro')) then
|
---|
384 | ityp=2
|
---|
385 | else if ((mynm.eq.'phe').or.(mynm.eq.'tyr').or.(mynm.eq.'trp'))
|
---|
386 | & then
|
---|
387 | ityp=3
|
---|
388 | endif
|
---|
389 | ihptype=ityp
|
---|
390 | return
|
---|
391 | end
|
---|
392 |
|
---|
393 | real*8 function ebiasrs(irsd)
|
---|
394 | include 'INCL.H'
|
---|
395 | include 'incl_lund.h'
|
---|
396 | dimension q1(2),q2(2)
|
---|
397 | data q1/-0.2,0.2/
|
---|
398 | data q2/0.42,-0.42/
|
---|
399 |
|
---|
400 | et=0.0
|
---|
401 | do i=0,1
|
---|
402 | iat1=iN(irsd)+i
|
---|
403 | do j=0,1
|
---|
404 | iat2=iC(irsd)+j
|
---|
405 | xij=xat(iat1)-xat(iat2)
|
---|
406 | yij=yat(iat1)-yat(iat2)
|
---|
407 | zij=zat(iat1)-zat(iat2)
|
---|
408 | et=et+q1(i+1)*q2(j+1)/sqrt(xij*xij+yij*yij+zij*zij)
|
---|
409 | enddo
|
---|
410 | enddo
|
---|
411 | ebiasrs=kbias*et
|
---|
412 | return
|
---|
413 | end
|
---|
414 | ! Evaluates backbone backbone hydrogen bond strength for residues
|
---|
415 | ! i and j, taking the donor from residue i and acceptor from residue j
|
---|
416 | real*8 function ehbmmrs(i,j)
|
---|
417 | include 'INCL.H'
|
---|
418 | include 'incl_lund.h'
|
---|
419 | double precision r2,r4,r6,dx,dy,dz,ca,cb
|
---|
420 | integer d1,d2,a1,a2
|
---|
421 | d1=iN(i)
|
---|
422 | d2=d1+1
|
---|
423 | a1=iC(j)+1 ! dipoles are numbered from -ve to +ve charge
|
---|
424 | a2=iC(j) ! so, acceptor 1 is the Oxygen, and a2, the carbon
|
---|
425 | dx=xat(a1)-xat(d2)
|
---|
426 | dy=yat(a1)-yat(d2)
|
---|
427 | dz=zat(a1)-zat(d2)
|
---|
428 | r2=dx*dx+dy*dy+dz*dz
|
---|
429 | if (r2.gt.cthb2) then
|
---|
430 | ! print *,'hbmm = 0 ',cthb2,r2,a1,a2,d1,d2
|
---|
431 | ! print *,'a1,a2,d1,d2,r2 = ',a1,a2,d1,d2,r2,sighb2,cthb
|
---|
432 | ehbmmrs=0
|
---|
433 | return
|
---|
434 | endif
|
---|
435 | ca=(xat(d2)-xat(d1))*dx+(yat(d2)-yat(d1))*dy+(zat(d2)-zat(d1))*dz
|
---|
436 | cb=(xat(a2)-xat(a1))*dx+(yat(a2)-yat(a1))*dy+(zat(a2)-zat(a1))*dz
|
---|
437 | if (powa.gt.0.and.ca.le.0) then
|
---|
438 | ! print *,'hbmm, returning 0 because of angle a'
|
---|
439 | ehbmmrs=0
|
---|
440 | return
|
---|
441 | endif
|
---|
442 | if (powb.gt.0.and.cb.le.0) then
|
---|
443 | ! print *,'hbmm, returning 0 because of angle b'
|
---|
444 | ehbmmrs=0
|
---|
445 | return
|
---|
446 | endif
|
---|
447 | r6=sighb2/r2
|
---|
448 | r4=r6*r6
|
---|
449 | r6=r6*r4
|
---|
450 | rdon2=(xat(d2)-xat(d1))**2+(yat(d2)-yat(d1))**2+
|
---|
451 | & (zat(d2)-zat(d1))**2
|
---|
452 | racc2=(xat(a2)-xat(a1))**2+(yat(a2)-yat(a1))**2+
|
---|
453 | & (zat(a2)-zat(a1))**2
|
---|
454 | evlu=((ca*ca/(r2*rdon2))**(0.5*powa))*
|
---|
455 | & ((cb*cb/(r2*racc2))**(0.5*powb))
|
---|
456 | evlu=evlu*(r6*(5*r6-6*r4)+alhb+blhb*r2)
|
---|
457 | ! print *,'found hbmm contribution ',i,j,epshb1,evlu
|
---|
458 | ehbmmrs=epshb1*evlu
|
---|
459 | return
|
---|
460 | end
|
---|
461 | real*8 function enylun(nml)
|
---|
462 | ! nml = 1 .. ntlml. No provision exists to handle out of range values
|
---|
463 | ! for nml inside this function.
|
---|
464 | include 'INCL.H'
|
---|
465 | include 'incl_lund.h'
|
---|
466 | character mynm*4
|
---|
467 | logical prlvr
|
---|
468 | eyhb=0.0 ! backbone-backbone and sidechain-backbone HB
|
---|
469 | eyel=0.0 ! Bias, or local electrostatic term
|
---|
470 | eysl=0.0 ! Hydrophobicity, replaces the solvent term of SMMP
|
---|
471 | eyvr=0.0 ! Local pair excluded volume, in a sense a variable potential
|
---|
472 | eyvw=0.0 ! atom-atom repulsion, excluded volume
|
---|
473 | ! atom-atom repulsion is calculated on a system wide basis, instead of
|
---|
474 | ! molecule by molecule for efficiency. Look into function exvlun.
|
---|
475 |
|
---|
476 | istres=irsml1(nml)
|
---|
477 | indres=irsml2(nml)
|
---|
478 |
|
---|
479 | ! First, all terms that can be calculated on a residue by residue basis
|
---|
480 | do i=istres,indres
|
---|
481 | mynm=seq(i)
|
---|
482 | call tolost(mynm)
|
---|
483 | if ((mynm.eq.'pro').or.(mynm.eq.'cpro')
|
---|
484 | & .or.(mynm.eq.'cpru').or.(mynm.eq.'prou')
|
---|
485 | & .or.(mynm.eq.'pron').or.(mynm.eq.'pro+')) then
|
---|
486 | prlvr=.true. ! residue i is a proline variant
|
---|
487 | else
|
---|
488 | prlvr=.false.
|
---|
489 | endif
|
---|
490 |
|
---|
491 | ! Bias, or local electrostatic term. Excluded from the list are
|
---|
492 | ! residues at the ends of the chain, glycine and all proline variants
|
---|
493 | if ((i.ne.istres).and.(i.ne.indres).and.
|
---|
494 | & .not.prlvr.and.mynm.ne.'gly') then
|
---|
495 | eyel=eyel+ebiasrs(i)
|
---|
496 | endif
|
---|
497 | ! Backbone--backbone hydrogen bonds
|
---|
498 | shbm1=1.0
|
---|
499 | shbm2=1.0
|
---|
500 | if ((i.eq.istres).or.(i.eq.indres)) shbm1=0.5
|
---|
501 | ! Residue i contributes the donor, and j, the acceptor, so both i and
|
---|
502 | ! j run over the whole set of amino acids.
|
---|
503 | ! No terms for residue i, if it is a proline variant.
|
---|
504 | if (.not.prlvr) then
|
---|
505 | do j=istres,indres
|
---|
506 | if ((j.lt.(i-2)).or.(j.gt.(i+1))) then
|
---|
507 | shbm2=1.0
|
---|
508 | if ((j.eq.istres).or.(j.eq.indres)) shbm2=0.5
|
---|
509 | etmp=ehbmmrs(i,j)
|
---|
510 | eyhb=eyhb+shbm1*shbm2*etmp
|
---|
511 | endif
|
---|
512 | enddo
|
---|
513 | endif
|
---|
514 | ! Hydrophobicity, only if residue i is hydrophobic to start with
|
---|
515 | ihpi=ihptype(i)
|
---|
516 | if (ihpi.ge.0) then
|
---|
517 | ! Unlike hydrogen bonds, the hydrophobicity potential is symmetric
|
---|
518 | ! in i and j. So, the loop for j runs from i+1 to the end.
|
---|
519 |
|
---|
520 | do j=i+1,indres
|
---|
521 | ihpj=ihptype(j)
|
---|
522 | if (ihpj.ge.0) then
|
---|
523 | etmp=ehp(i,j,ihpi,ihpj)
|
---|
524 | if (j.eq.(i+1)) etmp=0
|
---|
525 | if (j.eq.(i+2)) etmp=0.5*etmp
|
---|
526 | ! print *, 'hydrophobicity contribution ',etmp,i,j
|
---|
527 | eysl=eysl+etmp
|
---|
528 | endif
|
---|
529 | enddo
|
---|
530 | endif
|
---|
531 | enddo
|
---|
532 |
|
---|
533 | ! Terms that are not calculated residue by residue ...
|
---|
534 |
|
---|
535 | ! Local pair or third-neighbour excluded volume
|
---|
536 | ! Numerically this is normally the term with largest positive
|
---|
537 | ! contribution to the energy in an equilibrated stystem.
|
---|
538 |
|
---|
539 | i1=ilpst(nml)
|
---|
540 | i2=ilpnd(nml)
|
---|
541 | etmp=0.0
|
---|
542 | do i=i1,i2
|
---|
543 | etmp1=0.0
|
---|
544 | iat1=lcp1(i)
|
---|
545 | iat2=lcp2(i)
|
---|
546 | iatt1=ityat(iat1)
|
---|
547 | iatt2=ityat(iat2)
|
---|
548 | xij=xat(iat1)-xat(iat2)
|
---|
549 | yij=yat(iat1)-yat(iat2)
|
---|
550 | zij=zat(iat1)-zat(iat2)
|
---|
551 | r2=(xij*xij + yij*yij + zij*zij)
|
---|
552 | if (r2.le.exvcut2) then
|
---|
553 | r6=sig2lcp(iatt1,iatt2)/r2
|
---|
554 | r6=r6*r6*r6
|
---|
555 | etmp1=(r6*r6+asalcp(iatt1,iatt2)+bsalcp(iatt1,iatt2)*r2)
|
---|
556 | if (etmp1.ge.0) then
|
---|
557 | ! print *,'local pair contribution ',iat1,iat2,iatt1,
|
---|
558 | ! & iatt2,sqrt(sig2lcp(iatt1,iatt2)),etmp1
|
---|
559 | endif
|
---|
560 | etmp=etmp+etmp1
|
---|
561 | endif
|
---|
562 | ! print *,'pair : ',iat1,iat2,' contribution ',etmp1
|
---|
563 | ! print *,exvcut2,r2
|
---|
564 | enddo
|
---|
565 | eyvr=exvk*etmp
|
---|
566 | eysm=eyel+eyhb+eyvr+eysl
|
---|
567 | enylun=eysm
|
---|
568 | end
|
---|
569 | real*8 function eninlun()
|
---|
570 | include 'INCL.H'
|
---|
571 | eysmi=0.0
|
---|
572 | eyeli=0.0
|
---|
573 | eyvwi=0.0
|
---|
574 | eyhbi=0.0
|
---|
575 | eninlun=0.0
|
---|
576 | return
|
---|
577 | end
|
---|
578 | real*8 function ehp(i1,i2,ihp1,ihp2)
|
---|
579 | include 'INCL.H'
|
---|
580 | include 'incl_lund.h'
|
---|
581 | dimension r2min(12)
|
---|
582 |
|
---|
583 | b2=20.25
|
---|
584 | a2=12.25
|
---|
585 | ! ihp1=ihptype(i1)
|
---|
586 | ! ihp2=ihptype(i2)
|
---|
587 | if ((ihp1.le.0).or.(ihp2.le.0)) then
|
---|
588 | ehp=0.0
|
---|
589 | return
|
---|
590 | endif
|
---|
591 | ni=nhpat(i1)
|
---|
592 | nj=nhpat(i2)
|
---|
593 | do i=1,ni+nj
|
---|
594 | r2min(i)=100000000 ! quite far
|
---|
595 | enddo
|
---|
596 | do i=1,ni
|
---|
597 | k=ihpat(i1,i)
|
---|
598 | do j=1,nj
|
---|
599 | l=ihpat(i2,j)
|
---|
600 | xij=xat(k)-xat(l)
|
---|
601 | yij=yat(k)-yat(l)
|
---|
602 | zij=zat(k)-zat(l)
|
---|
603 | dtmp=(xij*xij + yij*yij + zij*zij)
|
---|
604 | if (dtmp.le.r2min(i)) r2min(i)=dtmp
|
---|
605 | if (dtmp.le.r2min(ni+j)) r2min(ni+j)=dtmp
|
---|
606 | enddo
|
---|
607 | enddo
|
---|
608 | ssum=0
|
---|
609 | do i=1,ni+nj
|
---|
610 | if (r2min(i).le.b2) then
|
---|
611 | if (r2min(i).lt.a2) then
|
---|
612 | ssum=ssum+1
|
---|
613 | else
|
---|
614 | ssum=ssum+(b2-r2min(i))/(b2-a2)
|
---|
615 | endif
|
---|
616 | endif
|
---|
617 | ! hpstrgth=hpstrg((ihp1-1)*nhptyp+ihp2)
|
---|
618 | ! print *, 'hp diagnosis ',ni,nj,ssum/(ni+nj),hpstrgth
|
---|
619 | enddo
|
---|
620 | ehp=-hpstrg((ihp1-1)*nhptyp+ihp2)*ssum/(ni+nj)
|
---|
621 | return
|
---|
622 | end
|
---|
623 |
|
---|
624 | real*8 function exvlun(nml)
|
---|
625 | include 'INCL.H'
|
---|
626 | include 'incl_lund.h'
|
---|
627 | ! For multi-chain systems it makes little sense to split the calculation
|
---|
628 | ! of this term into an 'interaction part' and a contribution from
|
---|
629 | ! individual molecules. So, normally this should always be called with
|
---|
630 | ! argument nml=0. Only for diagnostic reasons, you might want to find
|
---|
631 | ! the contribution from one molecule in a multi-chain system assuming
|
---|
632 | ! there was no other molecule.
|
---|
633 | dimension isort(mxat),ngbr(mxat),locccl(mxat),incell(mxcell)
|
---|
634 | dimension icell(mxat)
|
---|
635 | integer :: jx1, jy1, jz1
|
---|
636 | logical doit
|
---|
637 |
|
---|
638 | if (nml.eq.0) then
|
---|
639 | istat=iatrs1(irsml1(1))
|
---|
640 | indat=iatrs2(irsml2(ntlml))
|
---|
641 | else
|
---|
642 | istat=iatrs1(irsml1(nml))
|
---|
643 | indat=iatrs2(irsml2(nml))
|
---|
644 | endif
|
---|
645 |
|
---|
646 | eyvw=0.0
|
---|
647 | ! The beginning part of this implementation is very similar to the
|
---|
648 | ! assignment of cells to the atoms during calculation of solvent
|
---|
649 | ! accessible surface area. So, much of that part is similar. But
|
---|
650 | ! unlike the accessible surface calculations, this term is symmetric
|
---|
651 | ! in any two participating atoms. So, the part after the assignment
|
---|
652 | ! of cells differs even in the structure of the code.
|
---|
653 |
|
---|
654 | do i=1,mxcell
|
---|
655 | incell(i)=0
|
---|
656 | enddo
|
---|
657 | ! print *,'evaluating general excluded volume :',istat,',',indat
|
---|
658 | ! Find minimal containing box
|
---|
659 | xmin=xat(istat)
|
---|
660 | ymin=yat(istat)
|
---|
661 | zmin=zat(istat)
|
---|
662 | xmax=xmin
|
---|
663 | ymax=ymin
|
---|
664 | zmax=zmin
|
---|
665 |
|
---|
666 | do i=istat,indat
|
---|
667 | if (xat(i).le.xmin) then
|
---|
668 | xmin=xat(i)
|
---|
669 | else if (xat(i).ge.xmax) then
|
---|
670 | xmax=xat(i)
|
---|
671 | endif
|
---|
672 | if (yat(i).le.ymin) then
|
---|
673 | ymin=yat(i)
|
---|
674 | else if (yat(i).ge.ymax) then
|
---|
675 | ymax=yat(i)
|
---|
676 | endif
|
---|
677 | if (zat(i).le.zmin) then
|
---|
678 | zmin=zat(i)
|
---|
679 | else if (zat(i).ge.zmax) then
|
---|
680 | zmax=zat(i)
|
---|
681 | endif
|
---|
682 | enddo
|
---|
683 |
|
---|
684 | sizex=xmax-xmin
|
---|
685 | sizey=ymax-ymin
|
---|
686 | sizez=zmax-zmin
|
---|
687 | ! Number of cells along each directions that fit into the box.
|
---|
688 | ndx=int(sizex/exvcutg)+1
|
---|
689 | ndy=int(sizey/exvcutg)+1
|
---|
690 | ndz=int(sizez/exvcutg)+1
|
---|
691 |
|
---|
692 | nxy=ndx*ndy
|
---|
693 | ncell=nxy*ndz
|
---|
694 | ! print *,'Number of cells along x,y,z = ',ndx,',',ndy,',',ndz
|
---|
695 | if (ncell.ge.mxcell) then
|
---|
696 | print *,'exvlun> required number of cells',ncell,
|
---|
697 | & ' exceeded the limit ',mxcell
|
---|
698 | print *,'recompile with a higher mxcell.'
|
---|
699 | stop
|
---|
700 | endif
|
---|
701 | ! Expand box to contain an integral number of cells along each direction
|
---|
702 | shiftx=(dble(ndx)*exvcutg-sizex)/2.0
|
---|
703 | shifty=(dble(ndy)*exvcutg-sizey)/2.0
|
---|
704 | shiftz=(dble(ndz)*exvcutg-sizez)/2.0
|
---|
705 | xmin=xmin-shiftx
|
---|
706 | ymin=ymin-shifty
|
---|
707 | zmin=zmin-shiftz
|
---|
708 | xmax=xmax+shiftx
|
---|
709 | ymax=ymax+shifty
|
---|
710 | zmax=zmax+shiftz
|
---|
711 |
|
---|
712 | ! Set occupied cells to zero. Note that the maximum number of occupied
|
---|
713 | ! cells is the number of atoms in the system.
|
---|
714 | nocccl=0
|
---|
715 | do i=1,mxat
|
---|
716 | locccl(i)=0
|
---|
717 | enddo
|
---|
718 |
|
---|
719 | ! Put atoms in cells
|
---|
720 | do j=istat,indat
|
---|
721 | mx=min(int(max((xat(j)-xmin)/exvcutg,0.0d0)),ndx-1)
|
---|
722 | my=min(int(max((yat(j)-ymin)/exvcutg,0.0d0)),ndy-1)
|
---|
723 | mz=min(int(max((zat(j)-zmin)/exvcutg,0.0d0)),ndz-1)
|
---|
724 | icellj=mx+my*ndx+mz*nxy+1
|
---|
725 | icell(j)=icellj
|
---|
726 | if (icellj.gt.mxcell) then
|
---|
727 | print *,'exvlun> bad cell index ',icellj,' for atom ',j
|
---|
728 | stop
|
---|
729 | else
|
---|
730 | if (incell(icellj).eq.0) then
|
---|
731 | ! previously unoccupied cell
|
---|
732 | nocccl=nocccl+1
|
---|
733 | locccl(nocccl)=icellj
|
---|
734 | endif
|
---|
735 | incell(icellj)=incell(icellj)+1
|
---|
736 | endif
|
---|
737 | enddo
|
---|
738 | ! print *,'finished assigning cells. nocccl = ',nocccl
|
---|
739 | ! Cummulative occupancy of i'th cell
|
---|
740 | do i=1,ncell
|
---|
741 | incell(i+1)=incell(i+1)+incell(i)
|
---|
742 | enddo
|
---|
743 | ! print *,'finished making cumulative cell sums'
|
---|
744 | ! Sorting atoms by their cell index
|
---|
745 | do i=istat,indat
|
---|
746 | j=icell(i)
|
---|
747 | jj=incell(j)
|
---|
748 | isort(jj)=i
|
---|
749 | incell(j)=jj-1
|
---|
750 | enddo
|
---|
751 | ! print *,'sorted atoms by cell index'
|
---|
752 | etmp=0.0
|
---|
753 | do icl=1,nocccl
|
---|
754 | ! loop through occupied cells
|
---|
755 | lcell=locccl(icl)
|
---|
756 | ix=mod(lcell-1,ndx)
|
---|
757 | iz = (lcell - 1) / nxy
|
---|
758 | iy = ((lcell - 1) - iz * nxy) / ndx
|
---|
759 |
|
---|
760 | c print *,'icl=',icl,'absolute index of cell = ',lcell
|
---|
761 | c print *,'iz,iy,ix = ',iz,iy,ix
|
---|
762 | c find all atoms in current cell and all its forward-going neighbours
|
---|
763 | nex=ix+1
|
---|
764 | ney=iy+1
|
---|
765 | nez=iz+1
|
---|
766 | nsame=0
|
---|
767 | nngbr=0
|
---|
768 | do jx=ix,nex
|
---|
769 | if (jx.ge.ndx) then
|
---|
770 | jx1=0
|
---|
771 | else
|
---|
772 | jx1=jx
|
---|
773 | endif
|
---|
774 | do jy=iy,ney
|
---|
775 | if (jy.ge.ndy) then
|
---|
776 | jy1=0
|
---|
777 | else
|
---|
778 | jy1=jy
|
---|
779 | endif
|
---|
780 | do jz=iz,nez
|
---|
781 | if (jz.ge.ndz) then
|
---|
782 | jz1=0
|
---|
783 | else
|
---|
784 | jz1=jz
|
---|
785 | endif
|
---|
786 | jcl=jx1 + ndx*jy1 + nxy*jz1 + 1
|
---|
787 | ! write(*,*)'jcl,jx1,jy1,jz1:', jcl,jx1,jy1,jz1
|
---|
788 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
789 | ! count the total number of neighbours
|
---|
790 | nngbr=nngbr+1
|
---|
791 | if (jx.eq.ix.and.jy.eq.iy.and.jz.eq.iz) then
|
---|
792 | ! count how many neighbours are from the same cell
|
---|
793 | nsame=nsame+1
|
---|
794 | endif
|
---|
795 | ngbr(nngbr)=isort(ii)
|
---|
796 | enddo
|
---|
797 | enddo
|
---|
798 | enddo
|
---|
799 | enddo
|
---|
800 | ! A few more cells need to be searched, so that we cover 13 of the 26
|
---|
801 | ! neighbouring cells.
|
---|
802 | ! 1
|
---|
803 | jx=ix+1
|
---|
804 | if (jx.ge.ndx) jx=0
|
---|
805 | jy=iy
|
---|
806 | jz=iz-1
|
---|
807 | if (jz.lt.0) jz=ndz-1
|
---|
808 | jcl=jx+ndx*jy+nxy*jz+1
|
---|
809 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
810 | nngbr=nngbr+1
|
---|
811 | ngbr(nngbr)=isort(ii)
|
---|
812 | enddo
|
---|
813 | ! 2
|
---|
814 | jx=ix
|
---|
815 | jy=iy-1
|
---|
816 | if (jy.lt.0) jy =ndy-1
|
---|
817 | jz=iz+1
|
---|
818 | if (jz.ge.ndz) jz=0
|
---|
819 | jcl=jx+ndx*jy+nxy*jz+1
|
---|
820 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
821 | nngbr=nngbr+1
|
---|
822 | ngbr(nngbr)=isort(ii)
|
---|
823 | enddo
|
---|
824 | ! 3
|
---|
825 | jx=ix-1
|
---|
826 | if (jx.lt.0)jx =ndx-1
|
---|
827 | jy=iy+1
|
---|
828 | if (jy.ge.ndy) jy=0
|
---|
829 | jz=iz
|
---|
830 | jcl=jx+ndx*jy+nxy*jz+1
|
---|
831 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
832 | nngbr=nngbr+1
|
---|
833 | ngbr(nngbr)=isort(ii)
|
---|
834 | enddo
|
---|
835 | ! 4
|
---|
836 | jx=ix+1
|
---|
837 | if (jx.ge.ndx) jx=0
|
---|
838 | jy=iy+1
|
---|
839 | if (jy.ge.ndy) jy=0
|
---|
840 | jz=iz-1
|
---|
841 | if (jz.lt.0) jz=ndz-1
|
---|
842 | jcl=jx+ndx*jy+nxy*jz+1
|
---|
843 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
844 | nngbr=nngbr+1
|
---|
845 | ngbr(nngbr)=isort(ii)
|
---|
846 | enddo
|
---|
847 | ! 5
|
---|
848 | jx=ix+1
|
---|
849 | if (jx.ge.ndx) jx = 0
|
---|
850 | jy=iy-1
|
---|
851 | if (jy.lt.0) jy=ndy-1
|
---|
852 | jz=iz+1
|
---|
853 | if (jz.ge.ndz) jz=0
|
---|
854 | jcl=jx+ndx*jy+nxy*jz+1
|
---|
855 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
856 | nngbr=nngbr+1
|
---|
857 | ngbr(nngbr)=isort(ii)
|
---|
858 | enddo
|
---|
859 | ! 6
|
---|
860 | jx=ix+1
|
---|
861 | if (jx.ge.ndx) jx=0
|
---|
862 | jy=iy-1
|
---|
863 | if (jy.lt.0) jy=ndy-1
|
---|
864 | jz=iz-1
|
---|
865 | if (jz.lt.0) jz=ndy-1
|
---|
866 | jcl=jx+ndx*jy+nxy*jz+1
|
---|
867 | do ii=incell(jcl)+1,incell(jcl+1)
|
---|
868 | nngbr=nngbr+1
|
---|
869 | ngbr(nngbr)=isort(ii)
|
---|
870 | enddo
|
---|
871 |
|
---|
872 | ! print *,'atoms in same cell ',nsame
|
---|
873 | ! print *,'atoms in neighbouring cells ',nngbr
|
---|
874 | do i1=1,nsame
|
---|
875 | ! Over all atoms from the original cell
|
---|
876 | iat1=ngbr(i1)
|
---|
877 | do i2=i1,nngbr
|
---|
878 | ! Over all atoms in the original+neighbouring cells
|
---|
879 | iat2=ngbr(i2)
|
---|
880 | xij=xat(iat1)-xat(iat2)
|
---|
881 | yij=yat(iat1)-yat(iat2)
|
---|
882 | zij=zat(iat1)-zat(iat2)
|
---|
883 | r2=(xij*xij+yij*yij+zij*zij)
|
---|
884 |
|
---|
885 | if (r2.le.exvcutg2) then
|
---|
886 | doit=.false.
|
---|
887 | if (abs(iat2-iat1).gt.mxconr ) then
|
---|
888 | doit=.true.
|
---|
889 | else if (matcon(iat2-iat1,iat1).eq.1) then
|
---|
890 | doit=.true.
|
---|
891 | endif
|
---|
892 | if (doit) then
|
---|
893 | iatt1=ityat(iat1)
|
---|
894 | iatt2=ityat(iat2)
|
---|
895 | r6=sig2exv(iatt1,iatt2)/r2
|
---|
896 | r6=r6*r6*r6
|
---|
897 | etmp1=r6*r6+asaexv(iatt1,iatt2)
|
---|
898 | & +bsaexv(iatt1,iatt2)*r2
|
---|
899 | etmp=etmp+etmp1
|
---|
900 | ! if (etmp1.ge.2000) then
|
---|
901 | ! print *,'contribution ',iat1,iat2,etmp1
|
---|
902 | ! call outpdb(1,'EXAMPLES/clash.pdb')
|
---|
903 | ! stop
|
---|
904 | ! endif
|
---|
905 | endif
|
---|
906 | endif
|
---|
907 | enddo
|
---|
908 | enddo
|
---|
909 | enddo
|
---|
910 | ! irs=1
|
---|
911 | ! do iat=iatrs1(irs),iatrs2(irs)
|
---|
912 | ! do j=-mxconr,mxconr
|
---|
913 | ! print *,iat,j,':',matcon(j,iat)
|
---|
914 | ! enddo
|
---|
915 | ! enddo
|
---|
916 | ! irs=irsml2(1)
|
---|
917 | ! do iat=iatrs1(irs),iatrs2(irs)
|
---|
918 | ! do j=-mxconr,mxconr
|
---|
919 | ! print *,iat,j,':',matcon(j,iat)
|
---|
920 | ! enddo
|
---|
921 | ! enddo
|
---|
922 |
|
---|
923 | eyvw=exvk*etmp
|
---|
924 | exvlun=eyvw
|
---|
925 | return
|
---|
926 | end
|
---|
927 |
|
---|
928 | real*8 function exvbrfc()
|
---|
929 | ! Brute force excluded volume evaluation
|
---|
930 | include 'INCL.H'
|
---|
931 | include 'incl_lund.h'
|
---|
932 |
|
---|
933 | etmp=0.0
|
---|
934 | etmp1=0.0
|
---|
935 | print *,'max connection radius is ',mxconr
|
---|
936 | do iat1=iatrs1(irsml1(1)),iatrs2(irsml2(ntlml))
|
---|
937 | do iat2=iat1+1,iatrs2(irsml2(ntlml))
|
---|
938 | xij=xat(iat1)-xat(iat2)
|
---|
939 | yij=yat(iat1)-yat(iat2)
|
---|
940 | zij=zat(iat1)-zat(iat2)
|
---|
941 | r2=(xij*xij+yij*yij+zij*zij)
|
---|
942 |
|
---|
943 | if (r2.le.exvcutg2) then
|
---|
944 | if (abs(iat2-iat1).gt.mxconr.or.
|
---|
945 | & matcon(iat2-iat1,iat1).eq.1) then
|
---|
946 | iatt1=ityat(iat1)
|
---|
947 | iatt2=ityat(iat2)
|
---|
948 | r6=sig2exv(iatt1,iatt2)/r2
|
---|
949 | r6=r6*r6*r6
|
---|
950 | etmp1=r6*r6+asaexv(iatt1,iatt2)
|
---|
951 | & +bsaexv(iatt1,iatt2)*r2
|
---|
952 | etmp=etmp+etmp1
|
---|
953 | else
|
---|
954 | ! print *,'atoms ', iat1,' and ',iat2,' were close',
|
---|
955 | ! # 'but matcon is ',matcon(iat2-iat1,iat1)
|
---|
956 | endif
|
---|
957 | endif
|
---|
958 | enddo
|
---|
959 | enddo
|
---|
960 | exvbrfc=etmp*exvk
|
---|
961 | return
|
---|
962 | end
|
---|