| 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 iat1, iat2
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| 16 |
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| 17 | integer ires,frst,lst,root
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| 18 | do iat1=iCa(ires)+frst,iCa(ires)+lst
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| 19 | do iat2=iat1+1,iCa(ires)+lst
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| 20 | matcon(iat2-iat1,iat1)=0
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| 21 | matcon(iat1-iat2,iat2)=0
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| 22 | enddo
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| 23 | enddo
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| 24 | iat1=iCa(ires)+root
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| 25 | do iat2=iCa(ires)+root,iCa(ires)+lst
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| 26 | matcon(iat2-iat1,iat1)=0
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| 27 | matcon(iat1-iat2,iat2)=0
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| 28 | enddo
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| 29 | end subroutine set_local_constr
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| 30 |
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| 31 | subroutine init_lundff
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| 32 | include 'INCL.H'
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| 33 | include 'incl_lund.h'
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| 34 | double precision eunit, csacc
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| 35 |
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| 36 | integer i, j, iml, iat1, iat2, k, iat3, l, iat4, m, iat3p, irs
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| 37 | integer iatoff, iatmrg, ilp, lci
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| 38 |
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| 39 | character mynm*4
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| 40 | logical prlvr
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| 41 |
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| 42 | print *,'initializing Lund forcefield'
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| 43 | ! Some parameters in the Lund force field.
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| 44 | ! The correspondence between internal energy scale and kcal/mol
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| 45 | eunit=1.3315d0
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| 46 | ! eunit=1.0
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| 47 | ! Bias
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| 48 | kbias=100.0d0*eunit
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| 49 | ! print *,'Bias'
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| 50 | ! Hydrogen bonds
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| 51 | epshb1=3.1d0*eunit
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| 52 | epshb2=2.0d0*eunit
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| 53 | sighb=2.0d0
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| 54 | cthb=4.5d0
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| 55 | cthb2=cthb*cthb
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| 56 | powa=0.5d0
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| 57 | powb=0.5d0
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| 58 | blhb=-30.0d0*(((sighb/cthb)**10-(sighb/cthb)**12))/cthb2
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| 59 | alhb=-(5*((sighb/cthb)**12)-6*((sighb/cthb)**10))-blhb*cthb2
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| 60 | sighb2=sighb*sighb
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| 61 | cdon=1.0d0
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| 62 | cacc=(1.0d0/1.23d0)**powb
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| 63 | csacc=(1.0d0/1.25d0)**powb
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| 64 | ! print *,'Hydrogen bonds'
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| 65 | ! Hydrophobicity
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| 66 | ! print *,'Hydrophobicity with nhptyp = ',nhptyp
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| 67 |
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| 68 | hpstrg(1)=0.0d0*eunit
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| 69 | hpstrg(2)=0.1d0*eunit
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| 70 | hpstrg(3)=0.1d0*eunit
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| 71 | hpstrg(4)=0.1d0*eunit
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| 72 | hpstrg(5)=0.9d0*eunit
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| 73 | hpstrg(6)=2.8d0*eunit
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| 74 | hpstrg(7)=0.1d0*eunit
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| 75 | hpstrg(8)=2.8d0*eunit
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| 76 | hpstrg(9)=3.2d0*eunit
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| 77 |
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| 78 | do i=1,mxrs
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| 79 | do j=1,6
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| 80 | ihpat(i,j)=0
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| 81 | enddo
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| 82 | nhpat(i)=0
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| 83 | enddo
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| 84 | do i=irsml1(1),irsml2(ntlml)
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| 85 | mynm=seq(i)
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| 86 | call tolost(mynm)
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| 87 | if ((mynm.eq.'pro').or.(mynm.eq.'cpro')
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| 88 | & .or.(mynm.eq.'cpru').or.(mynm.eq.'prou')
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| 89 | & .or.(mynm.eq.'pron').or.(mynm.eq.'pro+')) then
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| 90 | prlvr=.true. ! residue i is a proline variant
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| 91 | print *, 'proline variant ',mynm,i
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| 92 | else
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| 93 | prlvr=.false.
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| 94 | endif
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| 95 |
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| 96 | if (mynm.eq.'ala') then
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| 97 | nhpat(i)=1
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| 98 | ihpat(i,1)=iCa(i)+2
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| 99 | else if (mynm.eq.'val') then
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| 100 | nhpat(i)=3
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| 101 | ihpat(i,1)=iCa(i)+2
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| 102 | ihpat(i,2)=iCa(i)+4
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| 103 | ihpat(i,3)=iCa(i)+8
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| 104 | else if (prlvr) then
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| 105 | nhpat(i)=3
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| 106 | ihpat(i,1)=iCa(i)+2
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| 107 | ihpat(i,2)=iCa(i)+5
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| 108 | ihpat(i,3)=iCa(i)+8
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| 109 | else if (mynm.eq.'leu') then
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| 110 | nhpat(i)=4
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| 111 | ihpat(i,1)=iCa(i)+2
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| 112 | ihpat(i,2)=iCa(i)+5
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| 113 | ihpat(i,3)=iCa(i)+7
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| 114 | ihpat(i,4)=iCa(i)+11
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| 115 | else if (mynm.eq.'ile') then
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| 116 | nhpat(i)=4
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| 117 | ihpat(i,1)=iCa(i)+2
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| 118 | ihpat(i,2)=iCa(i)+4
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| 119 | ihpat(i,3)=iCa(i)+8
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| 120 | ihpat(i,4)=iCa(i)+11
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| 121 | else if (mynm.eq.'met') then
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| 122 | nhpat(i)=4
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| 123 | ihpat(i,1)=iCa(i)+2
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| 124 | ihpat(i,2)=iCa(i)+5
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| 125 | ihpat(i,3)=iCa(i)+8
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| 126 | ihpat(i,4)=iCa(i)+9
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| 127 | else if (mynm.eq.'phe') then
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| 128 | nhpat(i)=6
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| 129 | ihpat(i,1)=iCa(i)+5
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| 130 | ihpat(i,2)=iCa(i)+6
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| 131 | ihpat(i,3)=iCa(i)+8
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| 132 | ihpat(i,4)=iCa(i)+10
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| 133 | ihpat(i,5)=iCa(i)+12
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| 134 | ihpat(i,6)=iCa(i)+14
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| 135 | else if (mynm.eq.'tyr') then
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| 136 | nhpat(i)=6
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| 137 | ihpat(i,1)=iCa(i)+5
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| 138 | ihpat(i,2)=iCa(i)+6
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| 139 | ihpat(i,3)=iCa(i)+8
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| 140 | ihpat(i,4)=iCa(i)+10
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| 141 | ihpat(i,5)=iCa(i)+13
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| 142 | ihpat(i,6)=iCa(i)+15
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| 143 | else if (mynm.eq.'trp') then
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| 144 | nhpat(i)=6
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| 145 | ihpat(i,1)=iCa(i)+10
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| 146 | ihpat(i,2)=iCa(i)+11
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| 147 | ihpat(i,3)=iCa(i)+13
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| 148 | ihpat(i,4)=iCa(i)+15
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| 149 | ihpat(i,5)=iCa(i)+17
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| 150 | ihpat(i,6)=iCa(i)+19
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| 151 | endif
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| 152 | enddo
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| 153 | ! print *,'Hydrophobicity'
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| 154 |
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| 155 | ! Excluded volume and local pair excluded volume terms
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| 156 | exvk=0.1*eunit
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| 157 | exvcut=4.3
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| 158 | exvcut2=exvcut*exvcut
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| 159 |
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| 160 | sigsa(1)=1.0d0 ! hydrogen
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| 161 | sigsa(2)=1.0d0 ! hydrogen
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| 162 | sigsa(3)=1.0d0 ! hydrogen
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| 163 | sigsa(4)=1.0d0 ! hydrogen
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| 164 | sigsa(5)=1.0d0 ! hydrogen
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| 165 | sigsa(6)=1.0d0 ! hydrogen
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| 166 | sigsa(7)=1.75d0 ! carbon
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| 167 | sigsa(8)=1.75d0 ! carbon
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| 168 | sigsa(9)=1.75d0 ! carbon
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| 169 | sigsa(10)=1.42d0 ! oxygen
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| 170 | sigsa(11)=1.42d0 ! oxygen
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| 171 | sigsa(12)=1.42d0 ! oxygen
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| 172 | sigsa(13)=1.55d0 ! nitrogen
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| 173 | sigsa(14)=1.55d0 ! nitrogen
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| 174 | sigsa(15)=1.55d0 ! nitrogen
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| 175 | sigsa(16)=1.77d0 ! sulfur
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| 176 | sigsa(17)=1.0d0 ! hydrogen
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| 177 | sigsa(18)=1.75d0 ! carbon
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| 178 |
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| 179 | do i=1,mxtyat
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| 180 | do j=1,mxtyat
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| 181 | sig2lcp(i,j)=(sigsa(i)+sigsa(j))**2
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| 182 | asalcp(i,j)=-7*((sig2lcp(i,j)/exvcut2)**6.0d0)
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| 183 | bsalcp(i,j)=6*((sig2lcp(i,j)/exvcut2)**6.0d0)/exvcut2
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| 184 | enddo
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| 185 | enddo
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| 186 | ! print *,'Local pair excluded volume constants'
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| 187 |
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| 188 | exvlam=0.75d0
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| 189 | exvcutg=exvcut*exvlam
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| 190 | exvcutg2=exvcutg*exvcutg
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| 191 |
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| 192 | do i=1,mxtyat
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| 193 | do j=1,mxtyat
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| 194 | sig2exv(i,j)=(exvlam*(sigsa(i)+sigsa(j)))**2
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| 195 | asaexv(i,j)=-7*((sig2exv(i,j)/exvcutg2)**6.0)
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| 196 | bsaexv(i,j)=6*((sig2exv(i,j)/exvcutg2)**6.0)/exvcutg2
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| 197 | enddo
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| 198 | enddo
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| 199 | ! print *,'General excluded volume constants'
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| 200 |
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| 201 | ! Initialization of the connections matrix matcon(i,j). The index
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| 202 | ! i runs from -mxconr to +mxconr, and j from 1 to mxat.
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| 203 | ! matcon(i2-i1,i1) = 0, if the distance between atoms i1 and i2 is fixed
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| 204 | ! = 2, if atoms i1 and i2 are separated by 3 covalent
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| 205 | ! bonds and their distance can change
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| 206 | ! = 1, for all other pairs
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| 207 | ! if abs(i2-i1) > mxconr, the atoms are assumed to be separated by
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| 208 | ! many bonds, and with no restriction on their distances. On a protein
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| 209 | ! molecule made of natural amino acids, atoms with indices separated
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| 210 | ! by more than 35 can not be connected by three covalent bonds.
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| 211 |
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| 212 | do i=1,mxat
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| 213 | do j=-mxconr,mxconr
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| 214 | matcon(j,i)=1
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| 215 | enddo
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| 216 | matcon(0,i)=0
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| 217 | enddo
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| 218 | ! continued...
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| 219 | do iml=1,ntlml
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| 220 | do iat1=iatrs1(irsml1(iml)),iatrs2(irsml2(iml))
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| 221 | do j=1,nbdat(iat1)
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| 222 | iat2=ibdat(j,iat1)
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| 223 | matcon(iat2-iat1,iat1)=0 ! directly bonded atoms
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| 224 | matcon(iat1-iat2,iat2)=0 !
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| 225 | do k=1,nbdat(iat2)
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| 226 | iat3=ibdat(k,iat2)
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| 227 | matcon(iat3-iat1,iat1)=0 !
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| 228 | matcon(iat1-iat3,iat3)=0 ! 2 covalent bonds
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| 229 | do l=1,nbdat(iat3)
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| 230 | iat4=ibdat(l,iat3)
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| 231 | if (iat4.ne.iat2) then
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| 232 | matcon(iat4-iat1,iat1)=2 !
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| 233 | matcon(iat1-iat4,iat4)=2 ! 3 covalent bonds
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| 234 | endif
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| 235 | do m=1,nbdat(iat2)
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| 236 | iat3p=ibdat(m,iat2)
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| 237 | if (iat3p.ne.iat3) then
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| 238 | matcon(iat4-iat3p,iat3p)=2 ! 3 covalent bonds
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| 239 | matcon(iat3p-iat4,iat4)=2 !
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| 240 | endif
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| 241 | enddo
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| 242 | enddo
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| 243 | enddo
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| 244 | do k=1,nbdat(iat1)
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| 245 | iat3=ibdat(k,iat1)
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| 246 | matcon(iat3-iat2,iat2)=0 ! also 2 bonds iat2-iat1-iat3
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| 247 | matcon(iat2-iat3,iat3)=0 !
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| 248 | enddo
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| 249 | enddo
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| 250 | enddo
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| 251 |
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| 252 | ! print *,'going to initialize connections for first residue'
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| 253 | ! print *,'iN,iCa,iC =',iN(irsml1(iml)),
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| 254 | ! # iCa(irsml1(iml)),iC(irsml1(iml))
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| 255 | do iat1=iN(irsml1(iml))+1,iCa(irsml1(iml))-1
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| 256 | ! print *,'connections for iat1 = ',iat1
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| 257 | matcon(iat1-iN(irsml1(iml)),iN(irsml1(iml)))=0
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| 258 | matcon(iN(irsml1(iml))-iat1,iat1)=0
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| 259 | matcon(iat1-iCa(irsml1(iml)),iCa(irsml1(iml)))=0
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| 260 | matcon(iCa(irsml1(iml))-iat1,iat1)=0
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| 261 | do iat2=iat1,iCa(irsml1(iml))-1
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| 262 | matcon(iat2-iat1,iat1)=0
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| 263 | matcon(iat1-iat2,iat2)=0
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| 264 | enddo
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| 265 | matcon(iat1-iCa(irsml1(iml))-1,iCa(irsml1(iml))+1)=2
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| 266 | matcon(iCa(irsml1(iml))+1-iat1,iat1)=2
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| 267 | matcon(iat1-iCa(irsml1(iml))-2,iCa(irsml1(iml))+2)=2
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| 268 | matcon(iCa(irsml1(iml))+2-iat1,iat1)=2
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| 269 | matcon(iat1-iC(irsml1(iml)),iC(irsml1(iml)))=2
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| 270 | matcon(iC(irsml1(iml))-iat1,iat1)=2
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| 271 | enddo
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| 272 |
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| 273 | ! Below: for certain residues, some atoms separated by 3 or more bonds
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| 274 | ! do not change distance. So, the connection matrix term for such pairs
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| 275 | ! should be zero.
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| 276 |
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| 277 | do irs=irsml1(iml),irsml2(iml)
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| 278 | if (irs.eq.irsml1(iml)) then
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| 279 | iatoff=1
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| 280 | else
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| 281 | iatoff=0
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| 282 | endif
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| 283 | if (irs.eq.irsml2(iml)) then
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| 284 | iatmrg=2
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| 285 | else
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| 286 | iatmrg=0
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| 287 | endif
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| 288 | mynm=seq(irs)
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| 289 | call tolost(mynm)
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| 290 | if ((mynm.eq.'pro')) then
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| 291 | prlvr=.true. ! residue i is a proline variant
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| 292 | else
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| 293 | prlvr=.false.
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| 294 | endif
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| 295 | if ((mynm.eq.'asn')) then
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| 296 | call set_local_constr(irs,5,9,2)
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| 297 | else if ((mynm.eq.'gln')) then
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| 298 | call set_local_constr(irs,8,12,5)
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| 299 | else if ((mynm.eq.'arg')) then
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| 300 | call set_local_constr(irs,11,19,8)
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| 301 | else if ((mynm.eq.'his')) then
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| 302 | call set_local_constr(irs,5,12,2)
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| 303 | else if (mynm.eq.'phe') then
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| 304 | call set_local_constr(irs,5,15,2)
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| 305 | else if (mynm.eq.'tyr') then
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| 306 | call set_local_constr(irs,5,16,2)
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| 307 | iat1=iCa(irs)+12 ! H_h
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| 308 | iat2=iCa(irs)+13 ! C_e2
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| 309 | iat3=iCa(irs)+8 ! C_e1
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| 310 | matcon(iat2-iat1,iat1)=2
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| 311 | matcon(iat1-iat2,iat2)=2
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| 312 | matcon(iat3-iat1,iat1)=2
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| 313 | matcon(iat1-iat3,iat3)=2
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| 314 | else if (mynm.eq.'trp') then
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| 315 | call set_local_constr(irs,5,19,2)
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| 316 | else if (prlvr) then
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| 317 | ! Proline. Many more distances are fixed because of the fixed
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| 318 | ! phi angle
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| 319 | call set_local_constr(irs,-3,11,-3)
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| 320 | matcon(iCa(irs-1)-iCa(irs)-8,iCa(irs)+8)=0
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| 321 | matcon(iCa(irs)+8-iCa(irs-1),iCa(irs-1))=0
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| 322 | endif
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| 323 | enddo
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| 324 |
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| 325 | ! Distances fixed because of the constant omega angle
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| 326 | do irs=irsml1(iml),irsml2(iml)-1
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| 327 | matcon(iCa(irs+1)-iC(irs)-1,iC(irs)+1)=0 ! O_i -- Ca_{i+1}
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| 328 | matcon(-iCa(irs+1)+iC(irs)+1,iCa(irs+1))=0 ! O_i -- Ca_{i+1}
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| 329 |
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| 330 | matcon(iN(irs+1)-iC(irs),iC(irs)+1)=0 ! O_i -- H_{i+1}
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| 331 | matcon(-iN(irs+1)+iC(irs),iN(irs+1)+1)=0 ! O_i -- H_{i+1}
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| 332 |
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| 333 | matcon(iCa(irs+1)-iCa(irs),iCa(irs))=0 ! Ca_i -- Ca_{i+1}
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| 334 | matcon(-iCa(irs+1)+iCa(irs),iCa(irs+1))=0 ! Ca_i -- Ca_{i+1}
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| 335 |
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| 336 | matcon(iN(irs+1)+1-iCa(irs),iCa(irs))=0 ! Ca_i -- H_{i+1}
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| 337 | matcon(-iN(irs+1)-1+iCa(irs),iN(irs+1)+1)=0 ! Ca_i -- H_{i+1}
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| 338 | enddo
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| 339 |
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| 340 | enddo
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| 341 | ! finished initializing matrix conmat
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| 342 | ! print *,'Connections matrix'
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| 343 | ! Local pair excluded volume
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| 344 | do i=1,mxml
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| 345 | ilpst(i)=1
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| 346 | ilpnd(i)=0
|
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| 347 | enddo
|
|---|
| 348 | do i=1,50*mxrs
|
|---|
| 349 | lcp1(i)=0
|
|---|
| 350 | lcp2(i)=0
|
|---|
| 351 | enddo
|
|---|
| 352 | ilp=0
|
|---|
| 353 | do iml=1,ntlml
|
|---|
| 354 | do iat1=iatrs1(irsml1(iml)),iatrs2(irsml2(iml))
|
|---|
| 355 | do iat2=iat1+1,iatrs2(irsml2(iml))
|
|---|
| 356 | if ((iat2-iat1.le.mxconr).and.
|
|---|
| 357 | & matcon(iat2-iat1,iat1).eq.2) then
|
|---|
| 358 | ilp=ilp+1
|
|---|
| 359 | lcp1(ilp)=iat1
|
|---|
| 360 | lcp2(ilp)=iat2
|
|---|
| 361 | endif
|
|---|
| 362 | enddo
|
|---|
| 363 | enddo
|
|---|
| 364 |
|
|---|
| 365 | ilpnd(iml)=ilp
|
|---|
| 366 | if (iml.lt.ntlml) then
|
|---|
| 367 | ilpst(iml+1)=ilp+1
|
|---|
| 368 | endif
|
|---|
| 369 | print *,'molecule ',iml,' lc pair range ',ilpst(iml),ilpnd(iml)
|
|---|
| 370 | ! print *,'local pair list'
|
|---|
| 371 | do lci=ilpst(iml),ilpnd(iml)
|
|---|
| 372 | iat1=lcp1(lci)
|
|---|
| 373 | iat2=lcp2(lci)
|
|---|
| 374 | ! print *,lci,iat1,iat2,ityat(iat1),ityat(iat2)
|
|---|
| 375 | enddo
|
|---|
| 376 | enddo
|
|---|
| 377 |
|
|---|
| 378 | print *,'finished initializing Lund force field'
|
|---|
| 379 | end
|
|---|
| 380 |
|
|---|
| 381 | integer function ihptype(iaa)
|
|---|
| 382 | include 'INCL.H'
|
|---|
| 383 | integer iaa, ityp
|
|---|
| 384 |
|
|---|
| 385 | character mynm*4
|
|---|
| 386 | mynm=seq(iaa)
|
|---|
| 387 | ityp=-1
|
|---|
| 388 | call tolost(mynm)
|
|---|
| 389 | if (mynm.eq.'ala') then
|
|---|
| 390 | ityp=1
|
|---|
| 391 | else if ((mynm.eq.'val').or.(mynm.eq.'leu').or.(mynm.eq.'ile')
|
|---|
| 392 | & .or.(mynm.eq.'met').or.(mynm.eq.'pro')) then
|
|---|
| 393 | ityp=2
|
|---|
| 394 | else if ((mynm.eq.'phe').or.(mynm.eq.'tyr').or.(mynm.eq.'trp'))
|
|---|
| 395 | & then
|
|---|
| 396 | ityp=3
|
|---|
| 397 | endif
|
|---|
| 398 | ihptype=ityp
|
|---|
| 399 | return
|
|---|
| 400 | end
|
|---|
| 401 |
|
|---|
| 402 | real*8 function ebiasrs(irsd)
|
|---|
| 403 | include 'INCL.H'
|
|---|
| 404 | include 'incl_lund.h'
|
|---|
| 405 | double precision q1, q2, et, xij, yij, zij
|
|---|
| 406 |
|
|---|
| 407 | integer i, iat1, irsd, j, iat2
|
|---|
| 408 |
|
|---|
| 409 | dimension q1(2),q2(2)
|
|---|
| 410 | data q1/-0.2,0.2/
|
|---|
| 411 | data q2/0.42,-0.42/
|
|---|
| 412 |
|
|---|
| 413 | et=0.0
|
|---|
| 414 | do i=0,1
|
|---|
| 415 | iat1=iN(irsd)+i
|
|---|
| 416 | do j=0,1
|
|---|
| 417 | iat2=iC(irsd)+j
|
|---|
| 418 | xij=xat(iat1)-xat(iat2)
|
|---|
| 419 | yij=yat(iat1)-yat(iat2)
|
|---|
| 420 | zij=zat(iat1)-zat(iat2)
|
|---|
| 421 | et=et+q1(i+1)*q2(j+1)/sqrt(xij*xij+yij*yij+zij*zij)
|
|---|
| 422 | enddo
|
|---|
| 423 | enddo
|
|---|
| 424 | ebiasrs=kbias*et
|
|---|
| 425 | return
|
|---|
| 426 | end
|
|---|
| 427 | ! Evaluates backbone backbone hydrogen bond strength for residues
|
|---|
| 428 | ! i and j, taking the donor from residue i and acceptor from residue j
|
|---|
| 429 | real*8 function ehbmmrs(i,j)
|
|---|
| 430 | include 'INCL.H'
|
|---|
| 431 | include 'incl_lund.h'
|
|---|
| 432 | double precision rdon2, racc2, evlu
|
|---|
| 433 |
|
|---|
| 434 | integer i, j
|
|---|
| 435 |
|
|---|
| 436 | double precision r2,r4,r6,dx,dy,dz,ca,cb
|
|---|
| 437 | integer d1,d2,a1,a2
|
|---|
| 438 | d1=iN(i)
|
|---|
| 439 | d2=d1+1
|
|---|
| 440 | a1=iC(j)+1 ! dipoles are numbered from -ve to +ve charge
|
|---|
| 441 | a2=iC(j) ! so, acceptor 1 is the Oxygen, and a2, the carbon
|
|---|
| 442 | dx=xat(a1)-xat(d2)
|
|---|
| 443 | dy=yat(a1)-yat(d2)
|
|---|
| 444 | dz=zat(a1)-zat(d2)
|
|---|
| 445 | r2=dx*dx+dy*dy+dz*dz
|
|---|
| 446 | if (r2.gt.cthb2) then
|
|---|
| 447 | ! print *,'hbmm = 0 ',cthb2,r2,a1,a2,d1,d2
|
|---|
| 448 | ! print *,'a1,a2,d1,d2,r2 = ',a1,a2,d1,d2,r2,sighb2,cthb
|
|---|
| 449 | ehbmmrs=0
|
|---|
| 450 | return
|
|---|
| 451 | endif
|
|---|
| 452 | ca=(xat(d2)-xat(d1))*dx+(yat(d2)-yat(d1))*dy+(zat(d2)-zat(d1))*dz
|
|---|
| 453 | cb=(xat(a2)-xat(a1))*dx+(yat(a2)-yat(a1))*dy+(zat(a2)-zat(a1))*dz
|
|---|
| 454 | if (powa.gt.0.and.ca.le.0) then
|
|---|
| 455 | ! print *,'hbmm, returning 0 because of angle a'
|
|---|
| 456 | ehbmmrs=0
|
|---|
| 457 | return
|
|---|
| 458 | endif
|
|---|
| 459 | if (powb.gt.0.and.cb.le.0) then
|
|---|
| 460 | ! print *,'hbmm, returning 0 because of angle b'
|
|---|
| 461 | ehbmmrs=0
|
|---|
| 462 | return
|
|---|
| 463 | endif
|
|---|
| 464 | r6=sighb2/r2
|
|---|
| 465 | r4=r6*r6
|
|---|
| 466 | r6=r6*r4
|
|---|
| 467 | rdon2=(xat(d2)-xat(d1))**2+(yat(d2)-yat(d1))**2+
|
|---|
| 468 | & (zat(d2)-zat(d1))**2
|
|---|
| 469 | racc2=(xat(a2)-xat(a1))**2+(yat(a2)-yat(a1))**2+
|
|---|
| 470 | & (zat(a2)-zat(a1))**2
|
|---|
| 471 | evlu=((ca*ca/(r2*rdon2))**(0.5*powa))*
|
|---|
| 472 | & ((cb*cb/(r2*racc2))**(0.5*powb))
|
|---|
| 473 | evlu=evlu*(r6*(5*r6-6*r4)+alhb+blhb*r2)
|
|---|
| 474 | ! print *,'found hbmm contribution ',i,j,epshb1,evlu
|
|---|
| 475 | ehbmmrs=epshb1*evlu
|
|---|
| 476 | return
|
|---|
| 477 | end
|
|---|
| 478 | real*8 function enylun(nml)
|
|---|
| 479 | ! nml = 1 .. ntlml. No provision exists to handle out of range values
|
|---|
| 480 | ! for nml inside this function.
|
|---|
| 481 | include 'INCL.H'
|
|---|
| 482 | include 'incl_lund.h'
|
|---|
| 483 | double precision ebiasrs, shbm1, shbm2, etmp, ehbmmrs, ehp, etmp1
|
|---|
| 484 | double precision xij, yij, zij, r2, r6
|
|---|
| 485 |
|
|---|
| 486 | integer istres, nml, indres, i, j, ihpi, ihptype, ihpj, i1, i2
|
|---|
| 487 | integer iat1, iat2, iatt1, iatt2
|
|---|
| 488 |
|
|---|
| 489 | character mynm*4
|
|---|
| 490 | logical prlvr
|
|---|
| 491 | eyhb=0.0 ! backbone-backbone and sidechain-backbone HB
|
|---|
| 492 | eyel=0.0 ! Bias, or local electrostatic term
|
|---|
| 493 | eysl=0.0 ! Hydrophobicity, replaces the solvent term of SMMP
|
|---|
| 494 | eyvr=0.0 ! Local pair excluded volume, in a sense a variable potential
|
|---|
| 495 | eyvw=0.0 ! atom-atom repulsion, excluded volume
|
|---|
| 496 | ! atom-atom repulsion is calculated on a system wide basis, instead of
|
|---|
| 497 | ! molecule by molecule for efficiency. Look into function exvlun.
|
|---|
| 498 |
|
|---|
| 499 | istres=irsml1(nml)
|
|---|
| 500 | indres=irsml2(nml)
|
|---|
| 501 |
|
|---|
| 502 | ! First, all terms that can be calculated on a residue by residue basis
|
|---|
| 503 | do i=istres,indres
|
|---|
| 504 | mynm=seq(i)
|
|---|
| 505 | call tolost(mynm)
|
|---|
| 506 | if ((mynm.eq.'pro').or.(mynm.eq.'cpro')
|
|---|
| 507 | & .or.(mynm.eq.'cpru').or.(mynm.eq.'prou')
|
|---|
| 508 | & .or.(mynm.eq.'pron').or.(mynm.eq.'pro+')) then
|
|---|
| 509 | prlvr=.true. ! residue i is a proline variant
|
|---|
| 510 | else
|
|---|
| 511 | prlvr=.false.
|
|---|
| 512 | endif
|
|---|
| 513 |
|
|---|
| 514 | ! Bias, or local electrostatic term. Excluded from the list are
|
|---|
| 515 | ! residues at the ends of the chain, glycine and all proline variants
|
|---|
| 516 | if ((i.ne.istres).and.(i.ne.indres).and.
|
|---|
| 517 | & .not.prlvr.and.mynm.ne.'gly') then
|
|---|
| 518 | eyel=eyel+ebiasrs(i)
|
|---|
| 519 | endif
|
|---|
| 520 | ! Backbone--backbone hydrogen bonds
|
|---|
| 521 | shbm1=1.0
|
|---|
| 522 | shbm2=1.0
|
|---|
| 523 | if ((i.eq.istres).or.(i.eq.indres)) shbm1=0.5
|
|---|
| 524 | ! Residue i contributes the donor, and j, the acceptor, so both i and
|
|---|
| 525 | ! j run over the whole set of amino acids.
|
|---|
| 526 | ! No terms for residue i, if it is a proline variant.
|
|---|
| 527 | if (.not.prlvr) then
|
|---|
| 528 | do j=istres,indres
|
|---|
| 529 | if ((j.lt.(i-2)).or.(j.gt.(i+1))) then
|
|---|
| 530 | shbm2=1.0
|
|---|
| 531 | if ((j.eq.istres).or.(j.eq.indres)) shbm2=0.5
|
|---|
| 532 | etmp=ehbmmrs(i,j)
|
|---|
| 533 | eyhb=eyhb+shbm1*shbm2*etmp
|
|---|
| 534 | endif
|
|---|
| 535 | enddo
|
|---|
| 536 | endif
|
|---|
| 537 | ! Hydrophobicity, only if residue i is hydrophobic to start with
|
|---|
| 538 | ihpi=ihptype(i)
|
|---|
| 539 | if (ihpi.ge.0) then
|
|---|
| 540 | ! Unlike hydrogen bonds, the hydrophobicity potential is symmetric
|
|---|
| 541 | ! in i and j. So, the loop for j runs from i+1 to the end.
|
|---|
| 542 |
|
|---|
| 543 | do j=i+1,indres
|
|---|
| 544 | ihpj=ihptype(j)
|
|---|
| 545 | if (ihpj.ge.0) then
|
|---|
| 546 | etmp=ehp(i,j,ihpi,ihpj)
|
|---|
| 547 | if (j.eq.(i+1)) etmp=0
|
|---|
| 548 | if (j.eq.(i+2)) etmp=0.5*etmp
|
|---|
| 549 | ! print *, 'hydrophobicity contribution ',etmp,i,j
|
|---|
| 550 | eysl=eysl+etmp
|
|---|
| 551 | endif
|
|---|
| 552 | enddo
|
|---|
| 553 | endif
|
|---|
| 554 | enddo
|
|---|
| 555 |
|
|---|
| 556 | ! Terms that are not calculated residue by residue ...
|
|---|
| 557 |
|
|---|
| 558 | ! Local pair or third-neighbour excluded volume
|
|---|
| 559 | ! Numerically this is normally the term with largest positive
|
|---|
| 560 | ! contribution to the energy in an equilibrated stystem.
|
|---|
| 561 |
|
|---|
| 562 | i1=ilpst(nml)
|
|---|
| 563 | i2=ilpnd(nml)
|
|---|
| 564 | etmp=0.0
|
|---|
| 565 | do i=i1,i2
|
|---|
| 566 | etmp1=0.0
|
|---|
| 567 | iat1=lcp1(i)
|
|---|
| 568 | iat2=lcp2(i)
|
|---|
| 569 | iatt1=ityat(iat1)
|
|---|
| 570 | iatt2=ityat(iat2)
|
|---|
| 571 | xij=xat(iat1)-xat(iat2)
|
|---|
| 572 | yij=yat(iat1)-yat(iat2)
|
|---|
| 573 | zij=zat(iat1)-zat(iat2)
|
|---|
| 574 | r2=(xij*xij + yij*yij + zij*zij)
|
|---|
| 575 | if (r2.le.exvcut2) then
|
|---|
| 576 | r6=sig2lcp(iatt1,iatt2)/r2
|
|---|
| 577 | r6=r6*r6*r6
|
|---|
| 578 | etmp1=(r6*r6+asalcp(iatt1,iatt2)+bsalcp(iatt1,iatt2)*r2)
|
|---|
| 579 | if (etmp1.ge.0) then
|
|---|
| 580 | ! print *,'local pair contribution ',iat1,iat2,iatt1,
|
|---|
| 581 | ! & iatt2,sqrt(sig2lcp(iatt1,iatt2)),etmp1
|
|---|
| 582 | endif
|
|---|
| 583 | etmp=etmp+etmp1
|
|---|
| 584 | endif
|
|---|
| 585 | ! print *,'pair : ',iat1,iat2,' contribution ',etmp1
|
|---|
| 586 | ! print *,exvcut2,r2
|
|---|
| 587 | enddo
|
|---|
| 588 | eyvr=exvk*etmp
|
|---|
| 589 | eysm=eyel+eyhb+eyvr+eysl
|
|---|
| 590 | enylun=eysm
|
|---|
| 591 | end
|
|---|
| 592 | real*8 function eninlun()
|
|---|
| 593 | include 'INCL.H'
|
|---|
| 594 | eysmi=0.0
|
|---|
| 595 | eyeli=0.0
|
|---|
| 596 | eyvwi=0.0
|
|---|
| 597 | eyhbi=0.0
|
|---|
| 598 | eninlun=0.0
|
|---|
| 599 | return
|
|---|
| 600 | end
|
|---|
| 601 | real*8 function ehp(i1,i2,ihp1,ihp2)
|
|---|
| 602 | include 'INCL.H'
|
|---|
| 603 | include 'incl_lund.h'
|
|---|
| 604 | double precision b2, a2, r2min, xij, yij, zij, dtmp, ssum
|
|---|
| 605 |
|
|---|
| 606 | integer ihp1, ihp2, ni, i1, nj, i2, i, k, j, l
|
|---|
| 607 |
|
|---|
| 608 | dimension r2min(12)
|
|---|
| 609 |
|
|---|
| 610 | b2=20.25
|
|---|
| 611 | a2=12.25
|
|---|
| 612 | ! ihp1=ihptype(i1)
|
|---|
| 613 | ! ihp2=ihptype(i2)
|
|---|
| 614 | if ((ihp1.le.0).or.(ihp2.le.0)) then
|
|---|
| 615 | ehp=0.0
|
|---|
| 616 | return
|
|---|
| 617 | endif
|
|---|
| 618 | ni=nhpat(i1)
|
|---|
| 619 | nj=nhpat(i2)
|
|---|
| 620 | do i=1,ni+nj
|
|---|
| 621 | r2min(i)=100000000 ! quite far
|
|---|
| 622 | enddo
|
|---|
| 623 | do i=1,ni
|
|---|
| 624 | k=ihpat(i1,i)
|
|---|
| 625 | do j=1,nj
|
|---|
| 626 | l=ihpat(i2,j)
|
|---|
| 627 | xij=xat(k)-xat(l)
|
|---|
| 628 | yij=yat(k)-yat(l)
|
|---|
| 629 | zij=zat(k)-zat(l)
|
|---|
| 630 | dtmp=(xij*xij + yij*yij + zij*zij)
|
|---|
| 631 | if (dtmp.le.r2min(i)) r2min(i)=dtmp
|
|---|
| 632 | if (dtmp.le.r2min(ni+j)) r2min(ni+j)=dtmp
|
|---|
| 633 | enddo
|
|---|
| 634 | enddo
|
|---|
| 635 | ssum=0
|
|---|
| 636 | do i=1,ni+nj
|
|---|
| 637 | if (r2min(i).le.b2) then
|
|---|
| 638 | if (r2min(i).lt.a2) then
|
|---|
| 639 | ssum=ssum+1
|
|---|
| 640 | else
|
|---|
| 641 | ssum=ssum+(b2-r2min(i))/(b2-a2)
|
|---|
| 642 | endif
|
|---|
| 643 | endif
|
|---|
| 644 | ! hpstrgth=hpstrg((ihp1-1)*nhptyp+ihp2)
|
|---|
| 645 | ! print *, 'hp diagnosis ',ni,nj,ssum/(ni+nj),hpstrgth
|
|---|
| 646 | enddo
|
|---|
| 647 | ehp=-hpstrg((ihp1-1)*nhptyp+ihp2)*ssum/(ni+nj)
|
|---|
| 648 | return
|
|---|
| 649 | end
|
|---|
| 650 |
|
|---|
| 651 | real*8 function exvlun(nml)
|
|---|
| 652 | include 'INCL.H'
|
|---|
| 653 | include 'incl_lund.h'
|
|---|
| 654 | ! For multi-chain systems it makes little sense to split the calculation
|
|---|
| 655 | ! of this term into an 'interaction part' and a contribution from
|
|---|
| 656 | ! individual molecules. So, normally this should always be called with
|
|---|
| 657 | ! argument nml=0. Only for diagnostic reasons, you might want to find
|
|---|
| 658 | ! the contribution from one molecule in a multi-chain system assuming
|
|---|
| 659 | ! there was no other molecule.
|
|---|
| 660 | double precision xmin, ymin, zmin, xmax, ymax, zmax, sizex, sizey
|
|---|
| 661 | double precision sizez, shiftx, shifty, shiftz, etmp, xij, yij
|
|---|
| 662 | double precision zij, r2, r6, etmp1
|
|---|
| 663 |
|
|---|
| 664 | integer nml, istat, indat, i, incell, ndx, ndy, ndz, nxy, ncell
|
|---|
| 665 | integer nocccl, locccl, j, mx, my, mz, icellj, icell, jj, isort
|
|---|
| 666 | integer icl, lcell, ix, iz, iy, nex, ney, nez, nsame, nngbr, jx
|
|---|
| 667 | integer jy, jz, jcl, ii, ngbr, i1, iat1, i2, iat2, iatt1, iatt2
|
|---|
| 668 |
|
|---|
| 669 | dimension isort(mxat),ngbr(mxat),locccl(mxat),incell(mxcell)
|
|---|
| 670 | dimension icell(mxat)
|
|---|
| 671 | integer :: jx1, jy1, jz1
|
|---|
| 672 |
|
|---|
| 673 | if (nml.eq.0) then
|
|---|
| 674 | istat=iatrs1(irsml1(1))
|
|---|
| 675 | indat=iatrs2(irsml2(ntlml))
|
|---|
| 676 | else
|
|---|
| 677 | istat=iatrs1(irsml1(nml))
|
|---|
| 678 | indat=iatrs2(irsml2(nml))
|
|---|
| 679 | endif
|
|---|
| 680 |
|
|---|
| 681 | eyvw=0.0
|
|---|
| 682 | ! The beginning part of this implementation is very similar to the
|
|---|
| 683 | ! assignment of cells to the atoms during calculation of solvent
|
|---|
| 684 | ! accessible surface area. So, much of that part is similar. But
|
|---|
| 685 | ! unlike the accessible surface calculations, this term is symmetric
|
|---|
| 686 | ! in any two participating atoms. So, the part after the assignment
|
|---|
| 687 | ! of cells differs even in the structure of the code.
|
|---|
| 688 |
|
|---|
| 689 | do i=1,mxcell
|
|---|
| 690 | incell(i)=0
|
|---|
| 691 | enddo
|
|---|
| 692 | ! print *,'evaluating general excluded volume :',istat,',',indat
|
|---|
| 693 | ! Find minimal containing box
|
|---|
| 694 | xmin=xat(istat)
|
|---|
| 695 | ymin=yat(istat)
|
|---|
| 696 | zmin=zat(istat)
|
|---|
| 697 | xmax=xmin
|
|---|
| 698 | ymax=ymin
|
|---|
| 699 | zmax=zmin
|
|---|
| 700 |
|
|---|
| 701 | do i=istat,indat
|
|---|
| 702 | if (xat(i).le.xmin) then
|
|---|
| 703 | xmin=xat(i)
|
|---|
| 704 | else if (xat(i).ge.xmax) then
|
|---|
| 705 | xmax=xat(i)
|
|---|
| 706 | endif
|
|---|
| 707 | if (yat(i).le.ymin) then
|
|---|
| 708 | ymin=yat(i)
|
|---|
| 709 | else if (yat(i).ge.ymax) then
|
|---|
| 710 | ymax=yat(i)
|
|---|
| 711 | endif
|
|---|
| 712 | if (zat(i).le.zmin) then
|
|---|
| 713 | zmin=zat(i)
|
|---|
| 714 | else if (zat(i).ge.zmax) then
|
|---|
| 715 | zmax=zat(i)
|
|---|
| 716 | endif
|
|---|
| 717 | enddo
|
|---|
| 718 |
|
|---|
| 719 | sizex=xmax-xmin
|
|---|
| 720 | sizey=ymax-ymin
|
|---|
| 721 | sizez=zmax-zmin
|
|---|
| 722 | ! Number of cells along each directions that fit into the box.
|
|---|
| 723 | ndx=int(sizex/exvcutg)+1
|
|---|
| 724 | ndy=int(sizey/exvcutg)+1
|
|---|
| 725 | ndz=int(sizez/exvcutg)+1
|
|---|
| 726 |
|
|---|
| 727 | nxy=ndx*ndy
|
|---|
| 728 | ncell=nxy*ndz
|
|---|
| 729 | ! print *,'Number of cells along x,y,z = ',ndx,',',ndy,',',ndz
|
|---|
| 730 | if (ncell.ge.mxcell) then
|
|---|
| 731 | print *,'exvlun> required number of cells',ncell,
|
|---|
| 732 | & ' exceeded the limit ',mxcell
|
|---|
| 733 | print *,'recompile with a higher mxcell.'
|
|---|
| 734 | stop
|
|---|
| 735 | endif
|
|---|
| 736 | ! Expand box to contain an integral number of cells along each direction
|
|---|
| 737 | shiftx=(dble(ndx)*exvcutg-sizex)/2.0
|
|---|
| 738 | shifty=(dble(ndy)*exvcutg-sizey)/2.0
|
|---|
| 739 | shiftz=(dble(ndz)*exvcutg-sizez)/2.0
|
|---|
| 740 | xmin=xmin-shiftx
|
|---|
| 741 | ymin=ymin-shifty
|
|---|
| 742 | zmin=zmin-shiftz
|
|---|
| 743 | xmax=xmax+shiftx
|
|---|
| 744 | ymax=ymax+shifty
|
|---|
| 745 | zmax=zmax+shiftz
|
|---|
| 746 |
|
|---|
| 747 | ! Set occupied cells to zero. Note that the maximum number of occupied
|
|---|
| 748 | ! cells is the number of atoms in the system.
|
|---|
| 749 | nocccl=0
|
|---|
| 750 | do i=1,mxat
|
|---|
| 751 | locccl(i)=0
|
|---|
| 752 | enddo
|
|---|
| 753 |
|
|---|
| 754 | ! Put atoms in cells
|
|---|
| 755 | do j=istat,indat
|
|---|
| 756 | mx=min(int(max((xat(j)-xmin)/exvcutg,0.0d0)),ndx-1)
|
|---|
| 757 | my=min(int(max((yat(j)-ymin)/exvcutg,0.0d0)),ndy-1)
|
|---|
| 758 | mz=min(int(max((zat(j)-zmin)/exvcutg,0.0d0)),ndz-1)
|
|---|
| 759 | icellj=mx+my*ndx+mz*nxy+1
|
|---|
| 760 | icell(j)=icellj
|
|---|
| 761 | if (icellj.gt.mxcell) then
|
|---|
| 762 | print *,'exvlun> bad cell index ',icellj,' for atom ',j
|
|---|
| 763 | stop
|
|---|
| 764 | else
|
|---|
| 765 | if (incell(icellj).eq.0) then
|
|---|
| 766 | ! previously unoccupied cell
|
|---|
| 767 | nocccl=nocccl+1
|
|---|
| 768 | locccl(nocccl)=icellj
|
|---|
| 769 | endif
|
|---|
| 770 | incell(icellj)=incell(icellj)+1
|
|---|
| 771 | endif
|
|---|
| 772 | enddo
|
|---|
| 773 | ! print *,'finished assigning cells. nocccl = ',nocccl
|
|---|
| 774 | ! Cummulative occupancy of i'th cell
|
|---|
| 775 | do i=1,ncell
|
|---|
| 776 | incell(i+1)=incell(i+1)+incell(i)
|
|---|
| 777 | enddo
|
|---|
| 778 | ! print *,'finished making cumulative cell sums'
|
|---|
| 779 | ! Sorting atoms by their cell index
|
|---|
| 780 | do i=istat,indat
|
|---|
| 781 | j=icell(i)
|
|---|
| 782 | jj=incell(j)
|
|---|
| 783 | isort(jj)=i
|
|---|
| 784 | incell(j)=jj-1
|
|---|
| 785 | enddo
|
|---|
| 786 | ! print *,'sorted atoms by cell index'
|
|---|
| 787 | etmp=0.0
|
|---|
| 788 | do icl=1,nocccl
|
|---|
| 789 | ! loop through occupied cells
|
|---|
| 790 | lcell=locccl(icl)
|
|---|
| 791 | ix=mod(lcell-1,ndx)
|
|---|
| 792 | iz = (lcell - 1) / nxy
|
|---|
| 793 | iy = ((lcell - 1) - iz * nxy) / ndx
|
|---|
| 794 |
|
|---|
| 795 | c print *,'icl=',icl,'absolute index of cell = ',lcell
|
|---|
| 796 | c print *,'iz,iy,ix = ',iz,iy,ix
|
|---|
| 797 | c find all atoms in current cell and all its forward-going neighbours
|
|---|
| 798 | nex=ix+1
|
|---|
| 799 | ney=iy+1
|
|---|
| 800 | nez=iz+1
|
|---|
| 801 | nsame=0
|
|---|
| 802 | nngbr=0
|
|---|
| 803 | do jx=ix,nex
|
|---|
| 804 | if (jx.ge.ndx) then
|
|---|
| 805 | jx1=0
|
|---|
| 806 | else
|
|---|
| 807 | jx1=jx
|
|---|
| 808 | endif
|
|---|
| 809 | do jy=iy,ney
|
|---|
| 810 | if (jy.ge.ndy) then
|
|---|
| 811 | jy1=0
|
|---|
| 812 | else
|
|---|
| 813 | jy1=jy
|
|---|
| 814 | endif
|
|---|
| 815 | do jz=iz,nez
|
|---|
| 816 | if (jz.ge.ndz) then
|
|---|
| 817 | jz1=0
|
|---|
| 818 | else
|
|---|
| 819 | jz1=jz
|
|---|
| 820 | endif
|
|---|
| 821 | jcl=jx1 + ndx*jy1 + nxy*jz1 + 1
|
|---|
| 822 | ! write (logString, *)'jcl,jx1,jy1,jz1:', jcl,jx1,jy1,jz1
|
|---|
| 823 | do ii=incell(jcl)+1,incell(jcl+1)
|
|---|
| 824 | ! count the total number of neighbours
|
|---|
| 825 | nngbr=nngbr+1
|
|---|
| 826 | if (jx.eq.ix.and.jy.eq.iy.and.jz.eq.iz) then
|
|---|
| 827 | ! count how many neighbours are from the same cell
|
|---|
| 828 | nsame=nsame+1
|
|---|
| 829 | endif
|
|---|
| 830 | ngbr(nngbr)=isort(ii)
|
|---|
| 831 | enddo
|
|---|
| 832 | enddo
|
|---|
| 833 | enddo
|
|---|
| 834 | enddo
|
|---|
| 835 | ! A few more cells need to be searched, so that we cover 13 of the 26
|
|---|
| 836 | ! neighbouring cells.
|
|---|
| 837 | ! 1
|
|---|
| 838 | jx=ix+1
|
|---|
| 839 | if (jx.ge.ndx) jx=0
|
|---|
| 840 | jy=iy
|
|---|
| 841 | jz=iz-1
|
|---|
| 842 | if (jz.lt.0) jz=ndz-1
|
|---|
| 843 | jcl=jx+ndx*jy+nxy*jz+1
|
|---|
| 844 | do ii=incell(jcl)+1,incell(jcl+1)
|
|---|
| 845 | nngbr=nngbr+1
|
|---|
| 846 | ngbr(nngbr)=isort(ii)
|
|---|
| 847 | enddo
|
|---|
| 848 | ! 2
|
|---|
| 849 | jx=ix
|
|---|
| 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 | ! 3
|
|---|
| 860 | jx=ix-1
|
|---|
| 861 | if (jx.lt.0)jx =ndx-1
|
|---|
| 862 | jy=iy+1
|
|---|
| 863 | if (jy.ge.ndy) jy=0
|
|---|
| 864 | jz=iz
|
|---|
| 865 | jcl=jx+ndx*jy+nxy*jz+1
|
|---|
| 866 | do ii=incell(jcl)+1,incell(jcl+1)
|
|---|
| 867 | nngbr=nngbr+1
|
|---|
| 868 | ngbr(nngbr)=isort(ii)
|
|---|
| 869 | enddo
|
|---|
| 870 | ! 4
|
|---|
| 871 | jx=ix+1
|
|---|
| 872 | if (jx.ge.ndx) jx=0
|
|---|
| 873 | jy=iy+1
|
|---|
| 874 | if (jy.ge.ndy) jy=0
|
|---|
| 875 | jz=iz-1
|
|---|
| 876 | if (jz.lt.0) jz=ndz-1
|
|---|
| 877 | jcl=jx+ndx*jy+nxy*jz+1
|
|---|
| 878 | do ii=incell(jcl)+1,incell(jcl+1)
|
|---|
| 879 | nngbr=nngbr+1
|
|---|
| 880 | ngbr(nngbr)=isort(ii)
|
|---|
| 881 | enddo
|
|---|
| 882 | ! 5
|
|---|
| 883 | jx=ix+1
|
|---|
| 884 | if (jx.ge.ndx) jx = 0
|
|---|
| 885 | jy=iy-1
|
|---|
| 886 | if (jy.lt.0) jy=ndy-1
|
|---|
| 887 | jz=iz+1
|
|---|
| 888 | if (jz.ge.ndz) jz=0
|
|---|
| 889 | jcl=jx+ndx*jy+nxy*jz+1
|
|---|
| 890 | do ii=incell(jcl)+1,incell(jcl+1)
|
|---|
| 891 | nngbr=nngbr+1
|
|---|
| 892 | ngbr(nngbr)=isort(ii)
|
|---|
| 893 | enddo
|
|---|
| 894 | ! 6
|
|---|
| 895 | jx=ix+1
|
|---|
| 896 | if (jx.ge.ndx) jx=0
|
|---|
| 897 | jy=iy-1
|
|---|
| 898 | if (jy.lt.0) jy=ndy-1
|
|---|
| 899 | jz=iz-1
|
|---|
| 900 | if (jz.lt.0) jz=ndy-1
|
|---|
| 901 | jcl=jx+ndx*jy+nxy*jz+1
|
|---|
| 902 | do ii=incell(jcl)+1,incell(jcl+1)
|
|---|
| 903 | nngbr=nngbr+1
|
|---|
| 904 | ngbr(nngbr)=isort(ii)
|
|---|
| 905 | enddo
|
|---|
| 906 |
|
|---|
| 907 | ! print *,'atoms in same cell ',nsame
|
|---|
| 908 | ! print *,'atoms in neighbouring cells ',nngbr
|
|---|
| 909 | do i1=1,nsame
|
|---|
| 910 | ! Over all atoms from the original cell
|
|---|
| 911 | iat1=ngbr(i1)
|
|---|
| 912 | do i2=i1,nngbr
|
|---|
| 913 | ! Over all atoms in the original+neighbouring cells
|
|---|
| 914 | iat2=ngbr(i2)
|
|---|
| 915 | xij=xat(iat1)-xat(iat2)
|
|---|
| 916 | yij=yat(iat1)-yat(iat2)
|
|---|
| 917 | zij=zat(iat1)-zat(iat2)
|
|---|
| 918 | r2=(xij*xij+yij*yij+zij*zij)
|
|---|
| 919 |
|
|---|
| 920 | if (r2.le.exvcutg2) then
|
|---|
| 921 | if (abs(iat2-iat1).gt.mxconr.or.
|
|---|
| 922 | & matcon(iat2-iat1,iat1).eq.1) then
|
|---|
| 923 | iatt1=ityat(iat1)
|
|---|
| 924 | iatt2=ityat(iat2)
|
|---|
| 925 | r6=sig2exv(iatt1,iatt2)/r2
|
|---|
| 926 | r6=r6*r6*r6
|
|---|
| 927 | etmp1=r6*r6+asaexv(iatt1,iatt2)
|
|---|
| 928 | & +bsaexv(iatt1,iatt2)*r2
|
|---|
| 929 | etmp=etmp+etmp1
|
|---|
| 930 | ! if (etmp1.ge.2000) then
|
|---|
| 931 | ! print *,'contribution ',iat1,iat2,etmp1
|
|---|
| 932 | ! call outpdb(1,'EXAMPLES/clash.pdb')
|
|---|
| 933 | ! stop
|
|---|
| 934 | ! endif
|
|---|
| 935 | endif
|
|---|
| 936 | endif
|
|---|
| 937 | enddo
|
|---|
| 938 | enddo
|
|---|
| 939 | enddo
|
|---|
| 940 | ! irs=1
|
|---|
| 941 | ! do iat=iatrs1(irs),iatrs2(irs)
|
|---|
| 942 | ! do j=-mxconr,mxconr
|
|---|
| 943 | ! print *,iat,j,':',matcon(j,iat)
|
|---|
| 944 | ! enddo
|
|---|
| 945 | ! enddo
|
|---|
| 946 | ! irs=irsml2(1)
|
|---|
| 947 | ! do iat=iatrs1(irs),iatrs2(irs)
|
|---|
| 948 | ! do j=-mxconr,mxconr
|
|---|
| 949 | ! print *,iat,j,':',matcon(j,iat)
|
|---|
| 950 | ! enddo
|
|---|
| 951 | ! enddo
|
|---|
| 952 |
|
|---|
| 953 | eyvw=exvk*etmp
|
|---|
| 954 | exvlun=eyvw
|
|---|
| 955 | return
|
|---|
| 956 | end
|
|---|
| 957 |
|
|---|
| 958 | real*8 function exvbrfc()
|
|---|
| 959 | ! Brute force excluded volume evaluation
|
|---|
| 960 | include 'INCL.H'
|
|---|
| 961 | include 'incl_lund.h'
|
|---|
| 962 |
|
|---|
| 963 | double precision etmp, etmp1, xij, yij, zij, r2, r6
|
|---|
| 964 |
|
|---|
| 965 | integer iat1, iat2, iatt1, iatt2
|
|---|
| 966 |
|
|---|
| 967 | etmp=0.0
|
|---|
| 968 | etmp1=0.0
|
|---|
| 969 | print *,'max connection radius is ',mxconr
|
|---|
| 970 | do iat1=iatrs1(irsml1(1)),iatrs2(irsml2(ntlml))
|
|---|
| 971 | do iat2=iat1+1,iatrs2(irsml2(ntlml))
|
|---|
| 972 | xij=xat(iat1)-xat(iat2)
|
|---|
| 973 | yij=yat(iat1)-yat(iat2)
|
|---|
| 974 | zij=zat(iat1)-zat(iat2)
|
|---|
| 975 | r2=(xij*xij+yij*yij+zij*zij)
|
|---|
| 976 |
|
|---|
| 977 | if (r2.le.exvcutg2) then
|
|---|
| 978 | if (abs(iat2-iat1).gt.mxconr.or.
|
|---|
| 979 | & matcon(iat2-iat1,iat1).eq.1) then
|
|---|
| 980 | iatt1=ityat(iat1)
|
|---|
| 981 | iatt2=ityat(iat2)
|
|---|
| 982 | r6=sig2exv(iatt1,iatt2)/r2
|
|---|
| 983 | r6=r6*r6*r6
|
|---|
| 984 | etmp1=r6*r6+asaexv(iatt1,iatt2)
|
|---|
| 985 | & +bsaexv(iatt1,iatt2)*r2
|
|---|
| 986 | etmp=etmp+etmp1
|
|---|
| 987 | else
|
|---|
| 988 | ! print *,'atoms ', iat1,' and ',iat2,' were close',
|
|---|
| 989 | ! # 'but matcon is ',matcon(iat2-iat1,iat1)
|
|---|
| 990 | endif
|
|---|
| 991 | endif
|
|---|
| 992 | enddo
|
|---|
| 993 | enddo
|
|---|
| 994 | exvbrfc=etmp*exvk
|
|---|
| 995 | return
|
|---|
| 996 | end
|
|---|
