[bd2278d] | 1 | !**************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: hbond,chhb,ishybd,
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| 4 | ! ishybdo,nursat,interhbond
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| 5 | !
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| 6 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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| 7 | ! Shura Hayryan, Chin-Ku
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| 8 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 9 | ! Jan H. Meinke, Sandipan Mohanty
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| 10 | !
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| 11 | ! **************************************************************
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[e40e335] | 12 |
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| 13 |
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| 14 | subroutine hbond(nml,mhb,ipr)
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[bd2278d] | 15 | ! .................................................................
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| 16 | ! PURPOSE: find hydrogen bonds in molecule 'nml'
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| 17 | !
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| 18 | ! prints HBonds, if ipr > 0
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| 19 | !
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| 20 | ! OUTPUT: mhb - number of hyd.bds. of type i->i+4
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| 21 | !
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| 22 | ! to INCL.H:
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| 23 | !
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| 24 | ! ntyhb - number of different types of hyd. bds. found
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| 25 | ! nutyhb - number of hyd.bds. found for each type
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| 26 | ! ixtyhb - index for each type of hyd. bd. composed as
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| 27 | ! (atom idx. of H) * 1000 + atm.idx. of acceptor
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| 28 | !
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| 29 | ! CALLS: chhb,ishybd (ishybdo),nursat
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| 30 | !
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| 31 | !................................................................
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[e40e335] | 32 |
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| 33 | include 'INCL.H'
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| 34 |
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[2019dff] | 35 | integer nml
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| 36 |
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| 37 | integer mhb
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| 38 |
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| 39 | integer nursat
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| 40 | double precision atbase
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| 41 |
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| 42 | integer ipr, i2s, i, i14, i1, i1s, i2, ia, ixhb, id, ifivr, ii, ih
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| 43 | integer ims, io, iv, ivw, ix, k, jj, j, n, na, nd, ntlvr, iat
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| 44 |
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[bd2278d] | 45 | !f2py intent(out) mhb
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[e40e335] | 46 | parameter (atbase=mxat)
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| 47 | logical ishb
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| 48 |
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| 49 |
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| 50 | do i=1,mxtyhb
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| 51 | nutyhb(i) = 0
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| 52 | ixtyhb(i) = 0
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| 53 | enddo
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| 54 | ntyhb=0
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| 55 | if (nml.eq.0) then
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| 56 | ntlvr = nvr
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| 57 | ifivr = ivrml1(1)
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| 58 | else
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| 59 | ntlvr=nvrml(nml)
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| 60 | if (ntlvr.eq.0) then
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| 61 | write (*,'(a,i4)')
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[bd2278d] | 62 | & ' hbond> No variables defined in molecule #',nml
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[e40e335] | 63 | return
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| 64 | endif
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| 65 |
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| 66 | ifivr=ivrml1(nml)
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[bd2278d] | 67 | ! Index of last moving set
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[e40e335] | 68 | i1s=imsml1(nml)+nmsml(nml)
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| 69 | endif
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[bd2278d] | 70 | ! Loop over all variables
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[e40e335] | 71 | do io=ifivr+ntlvr-1,ifivr,-1
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[bd2278d] | 72 | ! Get index of variable
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[e40e335] | 73 | iv=iorvr(io)
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[bd2278d] | 74 | ! Index of next to last moving set
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[e40e335] | 75 | i2s=i1s-1
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[bd2278d] | 76 | ! Index of moving set belonging to iv
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[e40e335] | 77 | i1s=imsvr1(iv)
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[bd2278d] | 78 | ! Loop over all moving sets between the one belonging to iv and the
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| 79 | ! next to last one
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[e40e335] | 80 | do ims=i1s,i2s
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[bd2278d] | 81 | ! First atom in moving set
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[e40e335] | 82 | i1=latms1(ims)
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[bd2278d] | 83 | ! Last atom in moving set
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[e40e335] | 84 | i2=latms2(ims)
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[bd2278d] | 85 | ! Loop over all atoms in moving set.
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[e40e335] | 86 | do i=i1,i2
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[bd2278d] | 87 | ! Loop over van der Waals domains of atom i
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[e40e335] | 88 | do ivw=ivwat1(i),ivwat2(i)
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[bd2278d] | 89 | ! Loop over atoms in van der Waals domain.
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[e40e335] | 90 | do j=lvwat1(ivw),lvwat2(ivw)
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| 91 |
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| 92 | call ishybd(i,j,ishb,ih,ia) ! Thornton criteria
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| 93 |
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| 94 | if (ishb) then
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| 95 |
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| 96 | ixhb=ih*atbase+ia
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| 97 |
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| 98 | do k=1,ntyhb
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| 99 | if (ixhb.eq.ixtyhb(k)) then
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| 100 | nutyhb(k)=nutyhb(k)+1
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| 101 | goto 1
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| 102 | endif
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| 103 | enddo
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| 104 |
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| 105 | if (ntyhb.lt.mxtyhb) then
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| 106 | ntyhb=ntyhb+1
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| 107 | nutyhb(ntyhb)=1
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| 108 | ixtyhb(ntyhb)=ixhb
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| 109 | else
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| 110 | write(*,*) ' hbond> increase parameter MXTYHB'
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| 111 | stop
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| 112 | endif
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| 113 |
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| 114 | endif ! have h.b.
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| 115 |
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| 116 | 1 enddo ! ... atoms j
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| 117 | enddo ! ... vdW-domains of i
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| 118 |
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| 119 | do i14=i14at1(i),i14at2(i) ! over 1-4 partners of 'i'
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| 120 | j=l14at(i14)
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| 121 |
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| 122 | call ishybd(i,j,ishb,ih,ia) ! Thornton criteria
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[bd2278d] | 123 | ! call ishybdo(i,j,ishb,ih,ia)
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[e40e335] | 124 |
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| 125 | if (ishb) then
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| 126 |
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| 127 | ixhb=ih*atbase+ia
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| 128 |
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| 129 | do k=1,ntyhb
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| 130 | if (ixhb.eq.ixtyhb(k)) then
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| 131 | nutyhb(k)=nutyhb(k)+1
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| 132 | goto 2
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| 133 | endif
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| 134 | enddo
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| 135 |
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| 136 | if (ntyhb.lt.mxtyhb) then
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| 137 | ntyhb=ntyhb+1
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| 138 | nutyhb(ntyhb)=1
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| 139 | ixtyhb(ntyhb)=ixhb
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| 140 | else
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| 141 | write(*,*) ' hbond> increase parameter MXTYHB'
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| 142 | stop
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| 143 | endif
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| 144 |
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| 145 | endif ! have h.b.
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| 146 |
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| 147 | 2 enddo ! ... 1-4-partners of i
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| 148 |
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| 149 | enddo ! ... atoms i
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| 150 | enddo ! ... m.s.
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| 151 |
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| 152 | enddo ! ... variables
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| 153 |
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| 154 | mhb=0
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| 155 |
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[bd2278d] | 156 | ! do inhb=1,ntyhb
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| 157 | ! mhb = mhb+nutyhb(inhb)
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| 158 | ! enddo
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[e40e335] | 159 |
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| 160 | if (ipr.gt.0) write(*,'(1x,a,/)') ' hbond> Hydrogen Bonds:'
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| 161 |
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| 162 | if (ntyhb.gt.0) then
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| 163 |
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| 164 | ii = 0
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| 165 | do i=1,ntyhb
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| 166 | jj = nutyhb(i)
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| 167 | do j = 1,jj
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| 168 | ii = ii + 1
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| 169 | ix = ixtyhb(ii)
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| 170 |
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| 171 | id =ix / atbase ! donor atom
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| 172 | nd = nursat(id) ! & residue
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| 173 |
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| 174 | ia = ix - id * atbase ! acceptor atom
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| 175 | na = nursat(ia)
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| 176 |
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| 177 | n = nd - na
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| 178 |
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| 179 | if (n.gt.4) mhb = mhb+1 ! only count these
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| 180 |
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| 181 | if (ipr.gt.0) then
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| 182 |
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| 183 | if (n.gt.0) then
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| 184 | write(*,'(1x,i3,a2,a4,a3,i3,1x,a4,a7,a4,a3,i3,1x,a4,a9,
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[bd2278d] | 185 | & i2)')
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| 186 | & ii,') ',nmat(ia),' ( ',na,seq(na),' ) <-- ',nmat(id),
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| 187 | & ' ( ', nd,seq(nd),' ) = i +',n
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[e40e335] | 188 | else
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| 189 | write(*,'(1x,i3,a2,a4,a3,i3,1x,a4,a7,a4,a3,i3,1x,a4,a9,
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[bd2278d] | 190 | & i2)')
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| 191 | & ii,') ',nmat(ia),' ( ',na,seq(na),' ) <-- ',nmat(id),
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| 192 | & ' ( ', nd,seq(nd),' ) = i -',abs(n)
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[e40e335] | 193 | endif
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| 194 |
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| 195 | call chhb(ia,id)
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| 196 | endif
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| 197 |
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| 198 | enddo
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| 199 | enddo
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| 200 | endif
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| 201 |
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| 202 | return
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| 203 | end
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[bd2278d] | 204 | ! .....................................................................
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| 205 | ! Calculates hydrogen bonds between different chains.
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| 206 | !
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| 207 | ! @return number of intermolecular hydrogen bonds. Returns 0 if only
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| 208 | ! one molecule is present. The value is returned in the
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| 209 | ! variable mhb.
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| 210 | !
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| 211 | ! @author Jan H. Meinke <j.meinke@fz-juelich.de>
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| 212 | !
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| 213 | ! .....................................................................
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[e40e335] | 214 | subroutine interhbond(mhb)
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| 215 |
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| 216 | include 'INCL.H'
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| 217 |
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[bd2278d] | 218 | !f2py intent(out) mhb
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[e40e335] | 219 |
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| 220 | logical ishb
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| 221 |
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| 222 | integer*4 mhb
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[2019dff] | 223 | integer iml, ires, jml, jat, jres
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| 224 |
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| 225 | integer ia, iat, ih
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| 226 |
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[e40e335] | 227 | mhb = 0
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| 228 | do iml = 1, ntlml
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| 229 | do jml = iml + 1, ntlml
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| 230 | mmhb(iml, jml) = 0
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| 231 | do ires= irsml1(iml), irsml2(iml)
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| 232 | do jres= irsml1(jml), irsml2(jml)
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| 233 | do iat = iatrs1(ires), iatrs2(ires)
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| 234 | do jat = iatrs1(jres), iatrs2(jres)
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| 235 | call ishybd(iat,jat,ishb,ih,ia)
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| 236 | if (ishb) then
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| 237 | mhb = mhb + 1
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| 238 | mmhb(iml, jml) = mmhb(iml, jml) + 1
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| 239 | endif
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| 240 | enddo ! jat
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| 241 | enddo ! iat
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| 242 | enddo ! jres
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| 243 | enddo ! ires
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| 244 | mmhb(jml, iml) = mmhb(iml, jml)
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| 245 | enddo ! jml
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| 246 | enddo ! iml
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| 247 |
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| 248 | end ! subroutine interhbond
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[bd2278d] | 249 | ! ************************
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[e40e335] | 250 | subroutine chhb(i,j)
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| 251 |
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| 252 | include 'INCL.H'
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[2019dff] | 253 | integer i
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| 254 |
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| 255 | integer j
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[e40e335] | 256 |
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[2019dff] | 257 | integer ih
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| 258 |
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| 259 | integer ia, ib, id, ihb
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| 260 |
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| 261 | double precision valang
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| 262 |
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| 263 | double precision cdah, cdad, adab, adha, ahab, dah, dad
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| 264 |
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[e40e335] | 265 | ihb = ihbty(ityat(i),ityat(j))
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| 266 |
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| 267 | if (ihb.gt.0) then
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| 268 | ih=i
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| 269 | ia=j
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| 270 | else
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| 271 | ih=j
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| 272 | ia=i
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| 273 | endif
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| 274 |
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| 275 | dah=sqrt((xat(ih)-xat(ia))**2+(yat(ih)-yat(ia))**2+
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[bd2278d] | 276 | & (zat(ih)-zat(ia))**2)
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[e40e335] | 277 |
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| 278 | id=iowat(ih)
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| 279 |
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| 280 | dad=sqrt((xat(id)-xat(ia))**2+(yat(id)-yat(ia))**2+
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[bd2278d] | 281 | & (zat(id)-zat(ia))**2)
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[e40e335] | 282 | adha=valang(id,ih,ia)*crd
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| 283 |
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| 284 | ib=iowat(ia)
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| 285 |
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| 286 | ahab=valang(ih,ia,ib)*crd
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| 287 | adab=valang(id,ia,ib)*crd
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| 288 |
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| 289 | write(*,*) ' '
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| 290 | write(*,*) ' Dah: ',dah,' Dad: ',dad
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| 291 | write(*,*) ' Adha: ',adha,' Ahab: ',adha,' Adab: ',adab
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| 292 | write(*,*) ' '
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| 293 |
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| 294 | return
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| 295 | end
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[bd2278d] | 296 | ! *************************************
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[e40e335] | 297 | subroutine ishybd(i,j,ishb,ih,ia)
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| 298 |
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| 299 |
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[bd2278d] | 300 | ! ..........................................................
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| 301 | ! PURPOSE: checks for hydrogen bond between atoms 'i' & 'j'
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| 302 | ! according to geometric criteria
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| 303 | !
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| 304 | ! OUTPUT: logical 'ishb' - true, if have Hydrogen bond
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| 305 | ! ih - index of Hydrogen atom
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| 306 | ! ia - index of Acceptor atom
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| 307 | !
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| 308 | ! [I.K.McDonald,J.M.Thornton,Satisfying hydrogen bond
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| 309 | ! potential in proteins.J.Mol.Biol.238(5),777-793 (1994)]
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| 310 | !
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| 311 | ! D: hydrogen(=H) donor, A: acceptor, B: atom bound to A
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| 312 | !
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| 313 | ! Dis_HA <= 2.5 & Dis_DA <= 3.9 & Angle(D-H-A) > 90 &
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| 314 | ! Angle(H-A-B) > 90 & Angle(D-A-B) > 90
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| 315 | ! ..........................................................
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[e40e335] | 316 |
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| 317 | include 'INCL.H'
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[2019dff] | 318 | double precision cdah, cang, cahb, cdad
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| 319 | integer i
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| 320 |
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| 321 | integer j
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[e40e335] | 322 |
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[2019dff] | 323 | integer ih
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| 324 |
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| 325 | integer ia, ib, id, ihb
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| 326 |
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| 327 | double precision valang
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| 328 |
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[e40e335] | 329 | parameter (cdad=3.9d0,
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[bd2278d] | 330 | & cdah=2.5d0,
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| 331 | & cang=110.d0)
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| 332 | ! # cang=90.d0)
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[e40e335] | 333 |
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| 334 | logical ishb
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| 335 |
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| 336 | cahb = cang * cdr
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| 337 | ishb = .false.
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| 338 |
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| 339 |
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| 340 | if (i.le.0.or.j.le.0) return
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| 341 |
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| 342 | ihb = ihbty(ityat(i),ityat(j))
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| 343 |
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| 344 | if (ihb.eq.0) then
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| 345 | return
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| 346 | elseif (ihb.gt.0) then
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| 347 | ih=i
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| 348 | ia=j
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| 349 | else
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| 350 | ih=j
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| 351 | ia=i
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| 352 | endif
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| 353 |
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| 354 | if (sqrt((xat(ih)-xat(ia))**2+(yat(ih)-yat(ia))**2+
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[bd2278d] | 355 | & (zat(ih)-zat(ia))**2).gt.cdah) return
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[e40e335] | 356 |
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| 357 | id=iowat(ih)
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| 358 |
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| 359 | if (id.le.0.or.sqrt((xat(id)-xat(ia))**2+(yat(id)-yat(ia))**2+
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[bd2278d] | 360 | & (zat(id)-zat(ia))**2).gt.cdad
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| 361 | & .or.valang(id,ih,ia).lt.cahb) return
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[e40e335] | 362 |
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| 363 | ib=iowat(ia)
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| 364 |
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| 365 | if (ib.gt.0.and.valang(ih,ia,ib).ge.cahb
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[bd2278d] | 366 | & .and.valang(id,ia,ib).ge.cahb) ishb=.true.
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[e40e335] | 367 |
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| 368 | return
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| 369 | end
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[bd2278d] | 370 | ! **************************************
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[e40e335] | 371 |
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| 372 | subroutine ishybdo(i,j,ishb,ih,ia)
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| 373 |
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[bd2278d] | 374 | ! ..........................................................
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| 375 | ! PURPOSE: checks for hydrogen bond between atoms 'i' & 'j'
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| 376 | ! according to geometric criteria
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| 377 | !
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| 378 | ! OUTPUT: logical 'ishb' - true, if have Hydrogen bond
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| 379 | ! ih - index of Hydrogen atom
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| 380 | ! ia - index of Acceptor atom
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| 381 | !
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| 382 | ! D: hydrogen(=H) donor, A: acceptor
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| 383 | !
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| 384 | ! Dis_AH <= 2.5 & Angle(D-H-A) >= 160
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| 385 | ! ...........................................................
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[e40e335] | 386 |
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| 387 | include 'INCL.H'
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[2019dff] | 388 | integer i
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| 389 |
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| 390 | integer j
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| 391 |
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| 392 | integer ih
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| 393 |
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| 394 | double precision cahb, cdah, cang, valang
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[e40e335] | 395 |
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[2019dff] | 396 | integer ia, ihb, id
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[e40e335] | 397 | parameter (cdah=2.5d0,
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[bd2278d] | 398 | & cang=140.d0)
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[e40e335] | 399 |
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| 400 | logical ishb
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| 401 |
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| 402 | cahb = cang * cdr
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| 403 |
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| 404 |
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| 405 | ishb = .false.
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| 406 |
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| 407 | if (i.le.0.or.j.le.0) return
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| 408 |
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| 409 | ihb = ihbty(ityat(i),ityat(j))
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| 410 |
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| 411 | if (ihb.eq.0) then
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| 412 | return
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| 413 | elseif (ihb.gt.0) then
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| 414 | ih=i
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| 415 | ia=j
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| 416 | else
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| 417 | ih=j
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| 418 | ia=i
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| 419 | endif
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| 420 |
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| 421 | if (sqrt((xat(ih)-xat(ia))**2+(yat(ih)-yat(ia))**2+
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[bd2278d] | 422 | & (zat(ih)-zat(ia))**2).gt.cdah) return
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[e40e335] | 423 |
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| 424 | id=iowat(ih)
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| 425 |
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| 426 | if (id.gt.0.and.valang(id,ih,ia).ge.cahb) ishb=.true.
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| 427 |
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| 428 | return
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| 429 | end
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| 430 |
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