1 | ! **************************************************************
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2 | !
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3 | ! This file contains the subroutines: enysol,tessel
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4 | !
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5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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6 | ! Shura Hayryan, Chin-Ku
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7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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8 | ! Jan H. Meinke, Sandipan Mohanty
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9 | !
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10 | ! **************************************************************
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11 |
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12 |
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13 | real*8 function enysol(nmol)
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14 |
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15 | include 'INCL.H'
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16 | ! --------------------------------------------------------------
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17 | !
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18 | ! Double Cubic Lattice algorithm for calculating the
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19 | ! solvation energy of proteins using
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20 | ! solvent accessible area method.
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21 | !
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22 | ! if nmol == 0 do solvation energy over all residues.
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23 | ! CALLS: nursat
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24 | !
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25 | ! -------------------------------------------------------------
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26 | ! TODO: Check the solvent energy for multiple molecules
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27 | ! arguments
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28 | integer nmol
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29 |
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30 | ! functions
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31 | integer nursat
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32 |
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33 | integer numbox, inbox, indsort, look, i, ii, ia, ib, ibox, icount
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34 | integer ilk, il, ik, ix, iy, iz, j, jy, jbox, jbi, jres, jj, jcnt
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35 | integer jtk, jx, jz, lbn, lst, mhx, mx, nsy, ndy, mz, my, nboxj
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36 | integer ndx, ncbox, nbt, nez, ndz, nex, ney, nlow, nhx, nnei
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37 | integer nrshi, nqxy, nrslow, mbt, nsx, nsz, numat, nup
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38 | double precision xyz, radb, radb2, ymin, diamax, area, akrad
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39 | double precision avr_x, avr_y, avr_z, dd, dr, dx, dy, dz, sizex
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40 | double precision rmax, shiftx, shifty, shiftz, sizey, sizez
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41 | double precision sizes, trad, zmin, xmax, xmin, ymax, zmax
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42 | double precision sdr, sdd, volume
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43 |
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44 | dimension numbox(mxat),inbox(mxbox+1),indsort(mxat),look(mxat)
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45 | dimension xyz(mxinbox,3),radb(mxinbox),radb2(mxinbox)
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46 | logical surfc(mxpoint)
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47 |
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48 | ! common/ressurf/surfres(mxrs)
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49 |
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50 | eyslh = 0.0
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51 | eyslp = 0.0
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52 | if (nmol.eq.0) then
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53 | nrslow=irsml1(1)
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54 | nrshi=irsml2(ntlml)
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55 | else
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56 | nrslow = irsml1(nmol)
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57 | nrshi = irsml2(nmol)
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58 | endif
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59 | nlow = iatrs1(nrslow)
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60 | nup = iatrs2(nrshi)
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61 | do i=nrslow,nrshi
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62 | surfres(i) = 0.0d0
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63 | end do
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64 |
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65 | numat= nup - nlow + 1
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66 |
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67 | do i=1,mxbox+1
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68 | inbox(i)=0
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69 | end do
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70 |
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71 | asa=0.0d0
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72 | vdvol=0.0d0
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73 | eysl=0.0d0
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74 |
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75 | avr_x=xat(nlow)
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76 | avr_y=yat(nlow)
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77 | avr_z=zat(nlow)
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78 | xmin=xat(nlow)
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79 | ymin=yat(nlow)
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80 | zmin=zat(nlow)
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81 | xmax=xmin
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82 | ymax=ymin
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83 | zmax=zmin
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84 |
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85 | rmax=rvdw(nlow)
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86 |
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87 | do j=nlow+1,nup
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88 | if(xat(j).le.xmin) then
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89 | xmin=xat(j)
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90 | else if(xat(j).ge.xmax) then
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91 | xmax=xat(j)
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92 | end if
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93 | avr_x=avr_x+xat(j)
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94 | if(yat(j).le.ymin) then
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95 | ymin=yat(j)
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96 | else if(yat(j).ge.ymax) then
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97 | ymax=yat(j)
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98 | end if
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99 | avr_y=avr_y+yat(j)
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100 | if(zat(j).le.zmin) then
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101 | zmin=zat(j)
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102 | else if(zat(j).ge.zmax) then
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103 | zmax=zat(j)
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104 | end if
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105 | avr_z=avr_z+zat(j)
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106 | if(rvdw(j).ge.rmax) rmax=rvdw(j)
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107 | end do
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108 |
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109 | avr_x=avr_x/dble(numat)
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110 | avr_y=avr_y/dble(numat)
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111 | avr_z=avr_z/dble(numat)
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112 | diamax=2.d0*rmax
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113 |
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114 | ! The sizes of the big box
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115 |
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116 | sizex=xmax-xmin
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117 | sizey=ymax-ymin
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118 | sizez=zmax-zmin
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119 |
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120 | ! How many maximal diameters in each size ?
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121 |
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122 | ndx=sizex/diamax + 1
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123 | ndy=sizey/diamax + 1
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124 | ndz=sizez/diamax + 1
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125 |
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126 | ! We may need the number of quadratic boxes in (X,Y) plane
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127 |
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128 | nqxy=ndx*ndy
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129 |
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130 | ! The number of cubic boxes of the size "diamax"
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131 |
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132 | ncbox=nqxy*ndz
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133 | if(ncbox.ge.mxbox) then
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134 | print *,'enysol> bad ncbox',ncbox
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135 | stop
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136 | end if
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137 |
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138 | ! Let us shift the borders to home all boxes
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139 |
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140 | shiftx=(dble(ndx)*diamax-sizex)/2.d0
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141 | shifty=(dble(ndy)*diamax-sizey)/2.d0
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142 | shiftz=(dble(ndz)*diamax-sizez)/2.d0
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143 | xmin=xmin-shiftx
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144 | ymin=ymin-shifty
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145 | zmin=zmin-shiftz
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146 | xmax=xmax+shiftx
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147 | ymax=ymax+shifty
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148 | zmax=zmax+shiftz
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149 |
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150 | ! Finding the box of each atom
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151 |
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152 | do j=nlow,nup
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153 | mx=min(int(max((xat(j)-xmin)/diamax,0.0d0)),ndx-1)
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154 | my=min(int(max((yat(j)-ymin)/diamax,0.0d0)),ndy-1)
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155 | mz=min(int(max((zat(j)-zmin)/diamax,0.0d0)),ndz-1)
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156 | nboxj=mx+my*ndx+mz*nqxy+1
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157 | numbox(j)=nboxj
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158 | if (nboxj.gt.mxbox) then
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159 | write(*,'(a)') 'enysol> bad mxboxe-2'
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160 | write(*,*) 'diagnostics ...'
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161 | write(*,*) 'atom ',j
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162 | write(*,*) 'position ',xat(j),yat(j),zat(j)
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163 | write(*,*) 'box indices ',mx,my,mz
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164 | write(*,*) 'resulting boxindex and limit ',nboxj,mxbox
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165 |
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166 | stop
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167 | else
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168 | inbox(nboxj)=inbox(nboxj)+1
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169 | end if
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170 | end do
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171 |
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172 | ! Summation over the boxes
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173 |
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174 | do i=1,ncbox
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175 | inbox(i+1)=inbox(i+1)+inbox(i)
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176 | end do
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177 |
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178 |
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179 | ! Sorting the atoms by the their box numbers
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180 |
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181 | do i=nlow,nup
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182 | j=numbox(i)
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183 | jj=inbox(j)
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184 | indsort(jj)=i
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185 | inbox(j)=jj-1
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186 | end do
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187 |
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188 | ! Getting started
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189 |
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190 | do iz=0,ndz-1 ! Over the boxes along Z-axis
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191 | do iy=0,ndy-1 !Over the boxes along Y-axis
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192 | do ix=0,ndx-1 !Over the boxes along X-axis
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193 |
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194 | ibox=ix+iy*ndx+iz*nqxy + 1
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195 |
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196 | ! Does this box contain atoms ?
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197 |
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198 | lbn=inbox(ibox+1)-inbox(ibox)
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199 |
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200 | if(lbn.gt.0) then ! There are some atoms
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201 | nsx=max(ix-1,0)
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202 | nsy=max(iy-1,0)
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203 | nsz=max(iz-1,0)
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204 | nex=min(ix+1,ndx-1)
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205 | ney=min(iy+1,ndy-1)
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206 | nez=min(iz+1,ndz-1)
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207 |
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208 | ! Atoms in the boxes around
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209 |
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210 | jcnt=1
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211 | do jz=nsz,nez
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212 | do jy=nsy,ney
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213 | do jx=nsx,nex
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214 | jbox=jx+jy*ndx+jz*nqxy+1
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215 | do ii=inbox(jbox)+1,inbox(jbox+1)
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216 | if(rvdw(indsort(ii)).gt.0.0d0) then
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217 | look(jcnt)=indsort(ii)
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218 | jcnt=jcnt+1
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219 | end if
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220 | end do
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221 | end do
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222 | end do
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223 | end do
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224 |
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225 | do ia=inbox(ibox)+1,inbox(ibox+1)
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226 | jbi=indsort(ia)
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227 | trad=rvdw(jbi)
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228 | if(trad.gt.0.0) then
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229 | nnei=0
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230 | do ib=1,jcnt-1
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231 | jtk=look(ib)
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232 | if(jtk.ne.jbi)then
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233 | dx=(xat(jbi)-xat(jtk))/trad
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234 | dy=(yat(jbi)-yat(jtk))/trad
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235 | dz=(zat(jbi)-zat(jtk))/trad
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236 | dd=dx*dx+dy*dy+dz*dz
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237 | akrad=rvdw(jtk)/trad
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238 | dr=1.0d0+akrad
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239 | dr=dr*dr
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240 | !c if contact
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241 | if(dd.le.dr) then
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242 | nnei=nnei+1
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243 | xyz(nnei,1)=dx
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244 | xyz(nnei,2)=dy
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245 | xyz(nnei,3)=dz
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246 | radb(nnei)=akrad
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247 | radb2(nnei)=akrad*akrad
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248 | end if
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249 | end if
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250 | end do
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251 | !c
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252 | do il=1,npnt
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253 | surfc(il)=.false.
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254 | end do
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255 |
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256 | ! Check overlap
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257 |
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258 | lst=1
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259 | do il=1,npnt
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260 | sdd = 0.0d0
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261 | do ilk=1,3
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262 | sdd = sdd +(xyz(lst,ilk)+spoint(il,ilk))**2
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263 | end do
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264 | if(sdd.gt.radb2(lst)) then
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265 | do ik=1,nnei
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266 | sdd =0.0d0
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267 | do ilk=1,3
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268 | sdd = sdd +(xyz(ik,ilk)+spoint(il,ilk))**2
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269 | end do
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270 | if(sdd.le.radb2(ik)) then
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271 | lst=ik
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272 | go to 99
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273 | end if
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274 | end do
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275 | 99 continue
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276 |
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277 | if(ik.gt.nnei)then
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278 | surfc(il)=.true.
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279 | end if
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280 | end if
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281 | end do
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282 |
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283 | icount=0
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284 | dx=0.0d0
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285 | dy=0.0d0
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286 | dz=0.0d0
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287 | do il=1,npnt
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288 | if(surfc(il)) then
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289 | icount=icount+1
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290 | dx=dx+spoint(il,1)
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291 | dy=dy+spoint(il,2)
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292 | dz=dz+spoint(il,3)
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293 | end if
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294 | end do
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295 | sdr=4.d0*pi*trad*trad/dble(npnt)
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296 | area = sdr*dble(icount)
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297 | volume = sdr/3.0d0*(trad*dble(icount)
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298 | & +(xat(jbi)-avr_x)*dx
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299 | & +(yat(jbi)-avr_y)*dy
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300 | & +(zat(jbi)-avr_z)*dz)
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301 |
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302 | asa=asa+area
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303 | vdvol=vdvol+volume
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304 | eysl=eysl+area*sigma(jbi)
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305 | ! Separate hydrophilic (h) and hyrdophobic (p) contributions to eysl
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306 | if (sigma(jbi).lt.0) then
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307 | eyslp = eyslp + area * sigma(jbi)
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308 | asap = asap + area
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309 | endif
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310 | if (sigma(jbi).gt.0) then
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311 | eyslh = eyslh + area * sigma(jbi)
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312 | asah = asah + area
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313 | endif
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314 | ! Measure how much a residue is solvent accessible:
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315 | jres = nursat(jbi)
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316 | surfres(jres) = surfres(jres) + area
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317 | end if
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318 | end do
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319 | end if
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320 | end do
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321 | end do
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322 | end do
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323 |
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324 | !
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325 | if (isolscl) then
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326 | nhx=0
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327 | mhx=0
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328 | nbt=0
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329 | mbt=0
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330 | call helix(nhx,mhx,nbt,mbt)
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331 | eysl=((nhx+nbt)*eysl)/(irsml2(ntlml)-irsml1(1))
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332 | endif
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333 |
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334 | enysol = eysl
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335 |
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336 | return
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337 | end
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338 | ! *********************
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339 | subroutine tessel
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340 | include 'INCL.H'
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341 | character lin*80
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342 | integer i
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343 | ! Skipping comment lines, which begin with '!'
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344 | read(20,'(a)') lin
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345 | do while(lin(1:1).eq.'!')
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346 | read (20,'(a)') lin
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347 | end do
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348 |
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349 | ! The first non-comment line is the number of the surface points
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350 |
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351 | read(lin(1:5),'(i5)') npnt
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352 | ! write(*,'(a,i5)') 'the number of points---->',npnt
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353 |
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354 | ! Read the surface points
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355 |
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356 | do i=1,npnt
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357 | read(20,'(3f20.10)') spoint(i,1),spoint(i,2),spoint(i,3)
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358 | ! write(31,'(3f20.10)') spoint(i,1),spoint(i,2),spoint(i,3)
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359 | end do
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360 |
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361 | return
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362 |
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363 | end
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364 |
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