| 1 | ! **************************************************************
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| 2 | !
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| 3 | !
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| 4 | ! This file contains the subroutines: addend, redchg, rplgrp
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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 | ! $Id: addend.f 334 2007-08-07 09:23:59Z meinke $
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| 12 | ! **************************************************************
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| 13 | subroutine addend(nml,grpn,grpc)
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| 14 |
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| 15 | ! ..............................................................
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| 16 | ! PURPOSE: modify terminal residues to complete bonding scheme
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| 17 | ! with residue 'grpn' at N- and residue 'grpc' at C-terminus
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| 18 | ! ! need initial co-ordinates for residues to modify
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| 19 | ! ! for N-terminus: may add only simple groups
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| 20 | !
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| 21 | ! CALLS: rplgrp,tolost,redchg
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| 22 | ! ..............................................................
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| 23 |
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| 24 | include 'INCL.H'
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| 25 |
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| 26 | character grpn*4,grpc*4
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| 27 |
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| 28 | character res*4,rpat*4,sbrs*4,grn*4,grc*4
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| 29 |
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| 30 | integer nml
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| 31 |
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| 32 | integer i, ifirs, ilars
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| 33 |
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| 34 | double precision cg
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| 35 |
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| 36 | grn = grpn
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| 37 | call tolost(grn)
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| 38 | grc = grpc
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| 39 | call tolost(grc)
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| 40 |
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| 41 | if (grn(:3).eq.'ace'.or.grc(:3).eq.'ace'
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| 42 | &.or.grn(:3).eq.'nme'.or.grc(:3).eq.'nme') then
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| 43 |
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| 44 | write (logString, '(2a)')
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| 45 | & ' addend> N-Acetyl (ace) or N-Methylamide (nme)',
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| 46 | & ' should be put in SEQUENCE file, not added as end groups'
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| 47 |
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| 48 | stop
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| 49 | endif
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| 50 |
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| 51 | ! __________________________________________ N-terminus
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| 52 | ifirs=irsml1(nml)
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| 53 | rpat='n '
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| 54 | res=seq(ifirs)
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| 55 | call tolost(res)
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| 56 | if (res(:3).ne.'ace') then
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| 57 | if (grn(:3).eq.'nh2') then
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| 58 | if (res(:3).eq.'hyp'.and..not.flex) then
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| 59 | if(sh2) then
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| 60 | sbrs='nh2+'
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| 61 | else
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| 62 | write (logString, '(2a)') ' addend> ',
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| 63 | & ' No N-terminal Hyp possible with ECEPP/3 dataset'
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| 64 | stop
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| 65 | endif
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| 66 |
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| 67 | elseif (res(:3).eq.'pro') then
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| 68 | sbrs='nh1 '
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| 69 | elseif (res(:3).eq.'gly'.and..not.flex) then
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| 70 | if (sh2) then
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| 71 | sbrs='nh2 '
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| 72 | else
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| 73 | sbrs='nh2g'
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| 74 | endif
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| 75 | else
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| 76 | sbrs='nh2 '
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| 77 | endif
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| 78 |
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| 79 | elseif (grn.eq.'nh3+') then
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| 80 | if (res(:3).eq.'pro'.and..not.flex) then
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| 81 | sbrs='nh2+'
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| 82 | elseif (res(:3).eq.'gly'.and..not.flex) then
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| 83 | sbrs='nh3g'
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| 84 | else
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| 85 | sbrs='nh3+'
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| 86 | endif
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| 87 |
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| 88 | else
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| 89 |
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| 90 | write (logString, '(2a)') ' addend> Can add only ',
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| 91 | & 'nh2 or nh3+ to N-terminus'
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| 92 | stop
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| 93 |
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| 94 | endif
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| 95 |
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| 96 | call rplgrp(nml,ifirs,rpat,sbrs)
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| 97 | if (flex) call redchg(nml,ifirs,rpat,sbrs) ! Flex dataset
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| 98 |
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| 99 | else ! ace
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| 100 |
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| 101 | write (logString, '(2a)') ' addend> Acetyl group',
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| 102 | & ' at N-terminus not modified'
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| 103 | endif
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| 104 |
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| 105 | ! __________________________________________ C-terminus
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| 106 | ilars=irsml2(nml)
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| 107 | rpat='c '
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| 108 | res=seq(ilars)
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| 109 | call tolost(res)
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| 110 |
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| 111 | if (res(:3).ne.'nme') then
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| 112 |
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| 113 | if (grc.eq.'cooh') then
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| 114 |
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| 115 | if (res(:3).eq.'gly'.and..not.sh2) then
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| 116 | sbrs='gooh'
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| 117 | else
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| 118 | sbrs='cooh'
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| 119 | endif
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| 120 |
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| 121 | elseif (grc.eq.'coo-') then
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| 122 |
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| 123 | if (res(:3).eq.'gly'.and..not.sh2) then
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| 124 | sbrs='goo-'
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| 125 | else
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| 126 | sbrs='coo-'
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| 127 | endif
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| 128 |
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| 129 | else
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| 130 |
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| 131 | write (logString, '(2a)') ' addend> Can add only ',
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| 132 | & 'cooh or coo- to C-terminus'
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| 133 | stop
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| 134 |
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| 135 | endif
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| 136 |
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| 137 | call rplgrp(nml,ilars,rpat,sbrs)
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| 138 | if (flex) call redchg(nml,ilars,rpat,sbrs) ! Flex dataset
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| 139 |
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| 140 | else ! N'-methylamide
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| 141 |
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| 142 | write (logString, '(2a)') ' addend> N-Methylamide',
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| 143 | & ' at C-terminus not modified'
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| 144 |
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| 145 | endif
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| 146 |
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| 147 | ! ----------------------------- net charge of molecule
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| 148 | cg = 0.d0
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| 149 | do i=iatrs1(irsml1(nml)),iatrs2(irsml2(nml))
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| 150 | cg = cg + cgat(i)
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| 151 | enddo
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| 152 | if (abs(cg).gt.1.d-5) then
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| 153 | write (logString, '(a,i2,a,f7.3)')
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| 154 | & ' addend> Net charge of molecule #'
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| 155 | & ,nml,': ',cg
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| 156 | endif
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| 157 |
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| 158 | return
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| 159 | end
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| 160 | ! ****************************************
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| 161 | subroutine rplgrp(nml,nrs,rpat,sbrs)
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| 162 |
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| 163 | ! ...............................................................
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| 164 | ! PURPOSE: replace atom(s) rooted at atom 'rpat' in residue
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| 165 | ! 'nrs' of molecule 'nml' by atom(s) rooted at
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| 166 | ! 'rpat' of residue 'sbrs' (same name of root
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| 167 | ! atom 'rpat' maintains bonding geometry for
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| 168 | ! preceeding atoms in 'nrs')
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| 169 | !
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| 170 | ! is NOT performed if 'rpat' is within mainchain,
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| 171 | ! except it is first/last mainchain atom of 'nml'
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| 172 | !
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| 173 | ! CALLS: dihedr,iopfil,iendst,eyring,fndbrn,redres,setsys,valang
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| 174 | ! ...............................................................
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| 175 |
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| 176 | include 'INCL.H'
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| 177 |
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| 178 | character rpat*4,sbrs*4
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| 179 | logical ntbb,bb
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| 180 | integer nml, nrs, ibd, iybd
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| 181 |
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| 182 | dimension ibd(mxbd+1),iybd(mxbd+1)
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| 183 |
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| 184 | integer iopfil, iendst
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| 185 |
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| 186 | double precision valang, dihedr
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| 187 |
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| 188 | integer ish, i, i1, irng1, irng2, ilavr, ilaat, i2, i3, ibdrg,
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| 189 | & ib, iat, ifirs, ifivr, ii, iow, isgbb1, ity, nfi, ilars,
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| 190 | & ivrrp, ivrsb, jsh, j, iybdrg, k, lvrrp, nb, natsb, nla,
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| 191 | & nfirp, nxt, nsb, nlarp, nfisb, nlasb, nrp, nsh,
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| 192 | & nvrsb, nxtbb1, nxtbb2, nxtsb
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| 193 | double precision ba, ca, ct, dx, dz, h3, h2, sa, st,to, x1, x2,
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| 194 | & x3, y1, y2, y3, z1, z2, z3
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| 195 |
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| 196 | ifirs=irsml1(nml)
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| 197 | ilars=irsml2(nml)
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| 198 |
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| 199 | nxt=ixatrs(nrs)
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| 200 | nfi=iatrs1(nrs)
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| 201 | nla=iatrs2(nrs)
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| 202 | ! __________________________ indices of atoms to be replaced
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| 203 | do i=nfi,nla
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| 204 | if (rpat.eq.nmat(i)) then
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| 205 | nfirp=i
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| 206 | goto 1
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| 207 | endif
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| 208 | enddo
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| 209 | write (logString, '(4a,i4,a,i4)') ' rplgrp> cannot find atom >',
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| 210 | & rpat,
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| 211 | & '< to be replaced in residue ',seq(nrs),nrs,' of molecule ',nml
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| 212 | stop
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| 213 |
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| 214 | 1 call fndbrn(nml,nrs,nfirp,nlarp,irng1,irng2,bb)
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| 215 | if (irng1.gt.0) goto 10
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| 216 | ntbb=.false.
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| 217 |
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| 218 | if (bb) then ! ..... backbone
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| 219 |
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| 220 | if (nfirp.eq.nxt.and.nrs.eq.ilars) goto 2 ! last mainchain atom
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| 221 |
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| 222 | if (nfirp.eq.nfi.and.nrs.eq.ifirs) then ! 1st MAINCHAIN ATOM !
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| 223 |
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| 224 | ntbb=.true.
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| 225 |
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| 226 | ibd(1)=iowat(nfirp)
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| 227 | iybd(1)=iyowat(nfirp)
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| 228 |
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| 229 | do i=1,mxbd
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| 230 | ibd(i+1)=ibdat(i,nfirp)
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| 231 | iybd(i+1)=iybdat(i,nfirp)
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| 232 | enddo
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| 233 |
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| 234 | ibdrg=0 ! __________________ check ring
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| 235 | iybdrg=1
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| 236 |
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| 237 | do i=1,nbdat(nfirp)+1
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| 238 | if (iowat(ibd(i)).ne.nfirp) then
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| 239 | if (ibdrg.ne.0) then
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| 240 | write (logString, '(2a,i3)')
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| 241 | & ' rplgrp> Can handle only simple ring at 1st',
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| 242 | & ' atom of molecule #',nml
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| 243 | stop
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| 244 | endif
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| 245 | ibdrg=ibd(i)
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| 246 | iybdrg=iybd(i)
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| 247 | endif
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| 248 | enddo
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| 249 | nxtbb1=nlarp+1 ! _________________ next backbone atoms
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| 250 | isgbb1=iyowat(nxtbb1)
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| 251 |
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| 252 | if (nxtbb1.eq.nxt) then
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| 253 | if (nrs.lt.ilars) then
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| 254 | nxtbb2=iatrs1(nrs+1)
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| 255 | goto 3
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| 256 | endif
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| 257 | else
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| 258 | do i=nxt,nxtbb1+1,-1
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| 259 | if (iowat(i).eq.nxtbb1) then
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| 260 | nxtbb2=i
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| 261 | goto 3
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| 262 | endif
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| 263 | enddo
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| 264 | endif
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| 265 | goto 11
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| 266 | else
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| 267 | write (logString, '(4a,i4,a,i4)')
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| 268 | & ' rplgrp> Cannot replace BACKBONE atom ',rpat,
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| 269 | & ' of residue ',seq(nrs),nrs,' in molecule #',nml
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| 270 | stop
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| 271 | endif
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| 272 |
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| 273 | endif ! N-terminus
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| 274 | ! _________________________________ previous atoms
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| 275 | 2 if (nfirp.eq.nfi.and.nrs.eq.ifirs) goto 11
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| 276 | nxtbb1=iowat(nfirp)
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| 277 | if (nxtbb1.eq.nfi.and.nrs.eq.ifirs) goto 11
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| 278 | nxtbb2=iowat(nxtbb1)
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| 279 | ! _______________________________ get data for substituent atoms
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| 280 | 3 if (iopfil(lunlib,reslib,'old','formatted').le.izero) then
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| 281 | write (logString, '(a,/,a,i3,2a)')
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| 282 | & ' rplgrp> ERROR opening library of residues:',
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| 283 | & ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib))
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| 284 | stop
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| 285 | endif
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| 286 | call redres(sbrs,natsb,nxtsb,nvrsb)
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| 287 | close (lunlib)
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| 288 | ! __________________________ indices of substituent atoms
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| 289 | do i=1,natsb
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| 290 | if (rpat.eq.nmath(i)) then
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| 291 | nfisb=i
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| 292 | goto 4
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| 293 | endif
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| 294 | enddo
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| 295 | write (logString, '(4a)') ' rplgrp> Cannot find atom >',rpat,
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| 296 | &'< in substituent residue ',sbrs
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| 297 | stop
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| 298 |
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| 299 | 4 nlasb=nfisb
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| 300 | do i=1,nbdath(nfisb)
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| 301 | ib=ibdath(i,nfisb)
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| 302 | if (iowath(ib).lt.nfisb) goto 10
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| 303 | do j=ib,natsb
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| 304 | if (j.gt.ib.and.iowath(j).lt.ib) goto 5
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| 305 | do k=1,nbdath(j)
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| 306 | if (ibdath(k,j).lt.nfisb) goto 10
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| 307 | enddo
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| 308 | nlasb=j
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| 309 | enddo ! ... branch atoms
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| 310 | 5 enddo ! ... branches
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| 311 | ! _________________________________________________ local axes at 'nfirp'
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| 312 | call setsys(nxtbb1,nfirp,nxtbb2,x1,x2,x3,y1,y2,y3,z1,z2,z3)
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| 313 |
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| 314 | xtoat(nfirp)=x1
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| 315 | ytoat(nfirp)=x2
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| 316 | ztoat(nfirp)=x3
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| 317 | xbaat(nfirp)=z1
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| 318 | ybaat(nfirp)=z2
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| 319 | zbaat(nfirp)=z3
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| 320 |
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| 321 | ! _____________________ add virtual atoms
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| 322 | if (ntbb) then
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| 323 |
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| 324 | ct=cstoat(nxtbb2) ! t.angle_(+2)
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| 325 | st=sntoat(nxtbb2)
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| 326 | ca=csbaat(nxtbb1) ! b.angle_(+1)
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| 327 | sa=snbaat(nxtbb1)
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| 328 |
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| 329 | ! ------------------- Eyring
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| 330 | h2=-sa*ct
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| 331 | h3=-sa*st
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| 332 | x1=-ca*x1+h2*y1+h3*z1
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| 333 | x2=-ca*x2+h2*y2+h3*z2
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| 334 | x3=-ca*x3+h2*y3+h3*z3
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| 335 | dx=one/sqrt(x1*x1+x2*x2+x3*x3)
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| 336 | x1=x1*dx
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| 337 | x2=x2*dx
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| 338 | x3=x3*dx
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| 339 |
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| 340 | xat(izero)=xat(nfirp)+x1
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| 341 | yat(izero)=yat(nfirp)+x2
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| 342 | zat(izero)=zat(nfirp)+x3
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| 343 | z1=-st*y1+ct*z1
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| 344 | z2=-st*y2+ct*z2
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| 345 | z3=-st*y3+ct*z3
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| 346 | dz=one/sqrt(z1*z1+z2*z2+z3*z3)
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| 347 | z1=z1*dz
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| 348 | z2=z2*dz
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| 349 | z3=z3*dz
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| 350 |
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| 351 | ct=cstoat(nxtbb1) ! t.angle_(+1)
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| 352 | st=sntoat(nxtbb1)
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| 353 |
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| 354 | ! -------------------- Eyring with b.angle = 90 deg.
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| 355 | xat(-ione)=xat(izero)-ct*(z2*x3-z3*x2)-st*z1
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| 356 | yat(-ione)=yat(izero)-ct*(z3*x1-z1*x3)-st*z2
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| 357 | zat(-ione)=zat(izero)-ct*(z1*x2-z2*x1)-st*z3
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| 358 |
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| 359 | endif
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| 360 | ! _____________________________________________ Shift atom data
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| 361 | nrp=nlarp-nfirp
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| 362 | nsb=nlasb-nfisb
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| 363 | if (nrp.ne.nsb) then
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| 364 | nsh=nsb-nrp
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| 365 | do i=nfi,nfirp-1 ! bonds to atoms after repl. group
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| 366 | do j=1,mxbd
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| 367 | ib=ibdat(j,i)
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| 368 | if (ib.gt.nlarp.and.ib.le.nla) ibdat(j,i)=ib+nsh
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| 369 | enddo
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| 370 | enddo
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| 371 | ilaat=iatrs2(irsml2(ntlml))
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| 372 | if (nrp.gt.nsb) then ! less atoms
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| 373 | i1=nlarp+1
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| 374 | i2=ilaat
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| 375 | i3=1
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| 376 | else ! more atoms
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| 377 | if ((ilaat+nsh).gt.mxat) then
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| 378 | write (logString, '(a,i5)') ' rplgrp> number of atoms > ',
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| 379 | & mxat
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| 380 | stop
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| 381 | endif
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| 382 |
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| 383 | i1=ilaat
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| 384 | i2=nlarp+1
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| 385 | i3=-1
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| 386 | endif
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| 387 |
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| 388 | do i=i1,i2,i3
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| 389 | ii=i+nsh
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| 390 | nbdat(ii)=nbdat(i)
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| 391 |
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| 392 | ibd(1)=iowat(i)
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| 393 | iybd(1)=iyowat(i)
|
|---|
| 394 | do j = 1,mxbd
|
|---|
| 395 | ibd(j+1)=ibdat(j,i)
|
|---|
| 396 | iybd(j+1)=iybdat(j,i)
|
|---|
| 397 | enddo
|
|---|
| 398 |
|
|---|
| 399 | do j=1,mxbd+1
|
|---|
| 400 | if (ibd(j).gt.nfirp) ibd(j)=ibd(j)+nsh
|
|---|
| 401 | enddo
|
|---|
| 402 |
|
|---|
| 403 | iowat(ii)=ibd(1)
|
|---|
| 404 | iyowat(ii)=iybd(1)
|
|---|
| 405 | do j = 1,mxbd
|
|---|
| 406 | ibdat(j,ii)=ibd(j+1)
|
|---|
| 407 | iybdat(j,ii)=iybd(j+1)
|
|---|
| 408 | enddo
|
|---|
| 409 |
|
|---|
| 410 | ityat(ii)=ityat(i)
|
|---|
| 411 | nmat(ii)=nmat(i)
|
|---|
| 412 | cgat(ii)=cgat(i)
|
|---|
| 413 | blat(ii)=blat(i)
|
|---|
| 414 | baat(ii)=baat(i)
|
|---|
| 415 | snbaat(ii)=snbaat(i)
|
|---|
| 416 | csbaat(ii)=csbaat(i)
|
|---|
| 417 | toat(ii)=toat(i)
|
|---|
| 418 | sntoat(ii)=sntoat(i)
|
|---|
| 419 | cstoat(ii)=cstoat(i)
|
|---|
| 420 | xat(ii)=xat(i)
|
|---|
| 421 | yat(ii)=yat(i)
|
|---|
| 422 | zat(ii)=zat(i)
|
|---|
| 423 | xtoat(ii)=xtoat(i)
|
|---|
| 424 | ytoat(ii)=ytoat(i)
|
|---|
| 425 | ztoat(ii)=ztoat(i)
|
|---|
| 426 | xbaat(ii)=xbaat(i)
|
|---|
| 427 | ybaat(ii)=ybaat(i)
|
|---|
| 428 | zbaat(ii)=zbaat(i)
|
|---|
| 429 |
|
|---|
| 430 | enddo
|
|---|
| 431 | ! ____________________________________________ Shift residue data
|
|---|
| 432 | do i=nrs+1,irsml2(ntlml)
|
|---|
| 433 | iatrs1(i)=iatrs1(i)+nsh
|
|---|
| 434 | iatrs2(i)=iatrs2(i)+nsh
|
|---|
| 435 | ixatrs(i)=ixatrs(i)+nsh
|
|---|
| 436 | enddo
|
|---|
| 437 | iatrs2(nrs)=nla+nsh
|
|---|
| 438 | if (nxt.gt.nlarp) ixatrs(nrs)=nxt+nsh
|
|---|
| 439 | else
|
|---|
| 440 | nsh=0
|
|---|
| 441 | endif
|
|---|
| 442 | ! _________________________________________ Correct data of 'nfirp'
|
|---|
| 443 | ish=nfirp-nfisb
|
|---|
| 444 | ityat(nfirp)=ityath(nfisb)
|
|---|
| 445 |
|
|---|
| 446 | if(.not.sh2) cgat(nfirp)=cgath(nfisb) ! NOT for 'ECEPP/2'
|
|---|
| 447 |
|
|---|
| 448 | nb=nbdath(nfisb) ! _______________ Bonds
|
|---|
| 449 |
|
|---|
| 450 | do i=1,mxbd
|
|---|
| 451 | ib=ibdath(i,nfisb)
|
|---|
| 452 | if (ib.ne.0) then
|
|---|
| 453 | ibd(i)=ib+ish
|
|---|
| 454 | iybd(i)=iybdath(i,nfisb)
|
|---|
| 455 | else
|
|---|
| 456 | ibd(i)=0
|
|---|
| 457 | iybd(i)=1
|
|---|
| 458 | endif
|
|---|
| 459 |
|
|---|
| 460 | enddo
|
|---|
| 461 |
|
|---|
| 462 | if (ntbb) then
|
|---|
| 463 |
|
|---|
| 464 | ibd(mxbd+1)=0
|
|---|
| 465 | iybd(mxbd+1)=1
|
|---|
| 466 |
|
|---|
| 467 | ibd(nb+1)=nxtbb1+nsh ! bond to next backbone atom
|
|---|
| 468 | iybd(nb+1)=isgbb1
|
|---|
| 469 |
|
|---|
| 470 | if (ibdrg.ne.0) then
|
|---|
| 471 | nb=nb+1
|
|---|
| 472 | if (nb.gt.mxbd) then
|
|---|
| 473 | write (logString, '(6a,/,2a,3(i4,a))')
|
|---|
| 474 | & ' rplgrp> Cannot add atoms following ',rpat,
|
|---|
| 475 | & ' from group ',sbrs,' to atom ',rpat,
|
|---|
| 476 | & ' of residue ',seq(nrs),nrs,' in molecule #',nml,
|
|---|
| 477 | & ' because need >',(mxbd+1),' bonds'
|
|---|
| 478 | stop
|
|---|
| 479 | endif
|
|---|
| 480 | ibd(nb+1)=ibdrg+nsh
|
|---|
| 481 | iybd(nb+1)=iybdrg
|
|---|
| 482 | endif
|
|---|
| 483 | iowat(nfirp)=ibd(1)
|
|---|
| 484 | iyowat(nfirp)=iybd(1)
|
|---|
| 485 | do i=1,mxbd
|
|---|
| 486 | ibdat(i,nfirp)=ibd(i+1)
|
|---|
| 487 | iybdat(i,nfirp)=iybd(i+1)
|
|---|
| 488 | enddo
|
|---|
| 489 | else ! not 'ntbb'
|
|---|
| 490 |
|
|---|
| 491 | do i=1,mxbd
|
|---|
| 492 | ibdat(i,nfirp)=ibd(i)
|
|---|
| 493 | iybdat(i,nfirp)=iybd(i)
|
|---|
| 494 | enddo
|
|---|
| 495 |
|
|---|
| 496 | endif
|
|---|
| 497 | nbdat(nfirp)=nb
|
|---|
| 498 | ! _________________________________________ Add data for substituent
|
|---|
| 499 | ii=nfirp
|
|---|
| 500 | do i=nfisb+1,nlasb
|
|---|
| 501 | ii=ii+1
|
|---|
| 502 | nbdat(ii)=nbdath(i)
|
|---|
| 503 |
|
|---|
| 504 | iow=iowath(i)+ish
|
|---|
| 505 | iowat(ii)=iow
|
|---|
| 506 | iyowat(ii)=iyowath(i)
|
|---|
| 507 |
|
|---|
| 508 | do j=1,mxbd
|
|---|
| 509 | ib=ibdath(j,i)
|
|---|
| 510 | if (ib.ge.nfisb) then
|
|---|
| 511 | ibdat(j,ii)=ib+ish
|
|---|
| 512 | else
|
|---|
| 513 | ibdat(j,ii)=ib
|
|---|
| 514 | endif
|
|---|
| 515 | iybdat(j,ii)=iybdath(j,i)
|
|---|
| 516 | enddo
|
|---|
| 517 |
|
|---|
| 518 | ityat(ii)=ityath(i)
|
|---|
| 519 | nmat(ii)=nmath(i)
|
|---|
| 520 | cgat(ii)=cgath(i)
|
|---|
| 521 | blat(ii)=blath(i)
|
|---|
| 522 | ba=baath(i)
|
|---|
| 523 | baat(ii)=ba
|
|---|
| 524 | csbaat(ii)=cos(ba)
|
|---|
| 525 | snbaat(ii)=sin(ba)
|
|---|
| 526 | to=toath(i)
|
|---|
| 527 | toat(ii)=to
|
|---|
| 528 | cstoat(ii)=cos(to)
|
|---|
| 529 | sntoat(ii)=sin(to)
|
|---|
| 530 | call eyring(ii,iow)
|
|---|
| 531 | if (ntbb) then ! reset some internal coordinates
|
|---|
| 532 | if (iow.eq.nfirp) then
|
|---|
| 533 | ba=valang(izero,nfirp,ii)
|
|---|
| 534 | baat(ii)=ba
|
|---|
| 535 | csbaat(ii)=cos(ba)
|
|---|
| 536 | snbaat(ii)=sin(ba)
|
|---|
| 537 | to=dihedr(-ione,izero,nfirp,ii)
|
|---|
| 538 | toat(ii)=to
|
|---|
| 539 | cstoat(ii)=cos(to)
|
|---|
| 540 | sntoat(ii)=sin(to)
|
|---|
| 541 | elseif (iowat(iow).eq.nfirp) then
|
|---|
| 542 | to=dihedr(izero,nfirp,iow,ii)
|
|---|
| 543 | toat(ii)=to
|
|---|
| 544 | cstoat(ii)=cos(to)
|
|---|
| 545 | sntoat(ii)=sin(to)
|
|---|
| 546 | endif
|
|---|
| 547 |
|
|---|
| 548 | endif ! ntbb
|
|---|
| 549 |
|
|---|
| 550 | enddo ! substituent atoms
|
|---|
| 551 | ! ___________________________________________________ Take care of Variables
|
|---|
| 552 | ! (assume variables of replaced group/substituent to be stored CONSECUTIVELY)
|
|---|
| 553 |
|
|---|
| 554 | ilavr=ivrml1(ntlml)+nvrml(ntlml)-1
|
|---|
| 555 | ifivr=ivrrs1(nrs) ! variables to be replaced (#=ivrrp,last=lvrrp)
|
|---|
| 556 | ivrrp=0
|
|---|
| 557 | do i=ifivr,ifivr+nvrrs(nrs)-1
|
|---|
| 558 | iat=iatvr(i)
|
|---|
| 559 | if (nfirp.lt.iat.and.iat.le.nlarp) then
|
|---|
| 560 | ivrrp=ivrrp+1
|
|---|
| 561 | lvrrp=i
|
|---|
| 562 | endif
|
|---|
| 563 | enddo
|
|---|
| 564 | if (ivrrp.eq.0) then ! No variables to replace
|
|---|
| 565 | do i=ifivr,ilavr
|
|---|
| 566 | if (iatvr(i).gt.nlarp) then
|
|---|
| 567 | lvrrp=i-1
|
|---|
| 568 | goto 6
|
|---|
| 569 | endif
|
|---|
| 570 | enddo
|
|---|
| 571 | lvrrp=ilavr
|
|---|
| 572 | endif
|
|---|
| 573 | 6 ivrsb=0 ! variables from substituent (#=ivrsb)
|
|---|
| 574 | do i=1,nvrsb
|
|---|
| 575 | iat=iatvrh(i)
|
|---|
| 576 | if (nfisb.lt.iat.and.iat.le.nlasb) then
|
|---|
| 577 | ity=ityvrh(i)
|
|---|
| 578 | if (ntbb.and.iowath(iat).eq.nfisb.and.ity.gt.2) goto 7
|
|---|
| 579 | ivrsb=ivrsb+1
|
|---|
| 580 | nmvrh(ivrsb)=nmvrh(i)
|
|---|
| 581 | ityvrh(ivrsb)=ityvrh(i)
|
|---|
| 582 | iclvrh(ivrsb)=iclvrh(i)
|
|---|
| 583 | iatvrh(ivrsb)=iat
|
|---|
| 584 | endif
|
|---|
| 585 | 7 enddo
|
|---|
| 586 | if (nsh.ne.0) then ! if # of atoms changed
|
|---|
| 587 | do i=lvrrp+1,ilavr
|
|---|
| 588 | iatvr(i)=iatvr(i)+nsh
|
|---|
| 589 | enddo
|
|---|
| 590 | endif
|
|---|
| 591 |
|
|---|
| 592 | if (ivrrp.ne.ivrsb) then ! shift data for variables
|
|---|
| 593 | jsh=ivrsb-ivrrp
|
|---|
| 594 | if (ivrrp.gt.ivrsb) then
|
|---|
| 595 | i1=lvrrp+1
|
|---|
| 596 | i2=ilavr
|
|---|
| 597 | i3=1
|
|---|
| 598 | else
|
|---|
| 599 | if ((ilavr+jsh).gt.mxvr) then
|
|---|
| 600 | write (logString, '(a,i5)')
|
|---|
| 601 | & ' rplgrp> number of variables > ',mxvr
|
|---|
| 602 | stop
|
|---|
| 603 | endif
|
|---|
| 604 | i1=ilavr
|
|---|
| 605 | i2=lvrrp+1
|
|---|
| 606 | i3=-1
|
|---|
| 607 | endif
|
|---|
| 608 | do i=i1,i2,i3
|
|---|
| 609 | ii=i+jsh
|
|---|
| 610 | ityvr(ii)=ityvr(i)
|
|---|
| 611 | iclvr(ii)=iclvr(i)
|
|---|
| 612 | nmvr(ii)=nmvr(i)
|
|---|
| 613 | iatvr(ii)=iatvr(i)
|
|---|
| 614 | enddo
|
|---|
| 615 |
|
|---|
| 616 | do i=nrs+1,irsml2(ntlml)
|
|---|
| 617 | ivrrs1(i)=ivrrs1(i)+jsh
|
|---|
| 618 | enddo
|
|---|
| 619 | nvrrs(nrs)=nvrrs(nrs)+jsh
|
|---|
| 620 | nvrml(nml)=nvrml(nml)+jsh
|
|---|
| 621 | do i=nml+1,ntlml
|
|---|
| 622 | ivrml1(i)=ivrml1(i)+jsh
|
|---|
| 623 | enddo
|
|---|
| 624 | endif
|
|---|
| 625 | ii=lvrrp-ivrrp ! Add variables for substitutent
|
|---|
| 626 | do i=1,ivrsb
|
|---|
| 627 | ii=ii+1
|
|---|
| 628 | nmvr(ii)=nmvrh(i)
|
|---|
| 629 | ityvr(ii)=ityvrh(i)
|
|---|
| 630 | iclvr(ii)=iclvrh(i)
|
|---|
| 631 | iatvr(ii)=iatvrh(i)+ish
|
|---|
| 632 | enddo
|
|---|
| 633 |
|
|---|
| 634 | return
|
|---|
| 635 | ! __________________________________________ Errors
|
|---|
| 636 | 10 write (logString, '(3a,/,2a,i4,a,i4,/,2a)')
|
|---|
| 637 | & ' rplgrp> Cannot replace atom(s) following ',rpat,
|
|---|
| 638 | & ' from INSIDE a ring',' in residue: ',seq(nrs),nrs,
|
|---|
| 639 | & ' in molecule #',nml,' or in substitute: ',sbrs
|
|---|
| 640 | stop
|
|---|
| 641 | 11 write (logString, '(4a,i4,a,i4,/,a)')
|
|---|
| 642 | & ' rplgrp> Cannot replace atom(s) following ',rpat,
|
|---|
| 643 | & ' of residue ',seq(nrs),nrs,' in molecule #',nml,
|
|---|
| 644 | & ' since necessary 2 previous atoms are not available'
|
|---|
| 645 | stop
|
|---|
| 646 |
|
|---|
| 647 | end
|
|---|
| 648 | ! ****************************************
|
|---|
| 649 | subroutine redchg(nml,nrs,rpat,sbrs)
|
|---|
| 650 |
|
|---|
| 651 | ! .........................................................
|
|---|
| 652 | ! PURPOSE: read and place atomic point charges from residue
|
|---|
| 653 | ! 'sbrs' to residue 'nrs' of molecule 'nml'
|
|---|
| 654 | ! from library 'chglib' with LUN=lunchg, if ilib=1
|
|---|
| 655 | ! 'reslib' with LUN=lunlib, if ilib=2
|
|---|
| 656 | !
|
|---|
| 657 | ! CALLS: iopfil,iendst,tolost
|
|---|
| 658 | ! ........................................................
|
|---|
| 659 |
|
|---|
| 660 | include 'INCL.H'
|
|---|
| 661 |
|
|---|
| 662 | character rpat*4,sbrs*4,atnm*4,res*4,cgty*5,line*100
|
|---|
| 663 | integer nml, nrs
|
|---|
| 664 |
|
|---|
| 665 | integer iopfil, iendst
|
|---|
| 666 |
|
|---|
| 667 | integer ifirs, ilars, ifvr, ilib, i, l, j, nchg
|
|---|
| 668 |
|
|---|
| 669 | ifirs=irsml1(nml)
|
|---|
| 670 | ilars=irsml2(nml)
|
|---|
| 671 | res=seq(nrs)
|
|---|
| 672 | call tolost(res)
|
|---|
| 673 |
|
|---|
| 674 | if (nrs.eq.ifirs.or.nrs.eq.ilars) then
|
|---|
| 675 |
|
|---|
| 676 | if (rpat.eq.'n '.or.rpat.eq.'c ') then
|
|---|
| 677 | if (nrs.eq.ifirs.and.nrs.eq.ilars) goto 10 ! Dont have this yet
|
|---|
| 678 |
|
|---|
| 679 | if (rpat.eq.'n '.and.nrs.eq.ifirs) then
|
|---|
| 680 | if (res(1:3).eq.'pro'.or.res(1:3).eq.'hyp') then
|
|---|
| 681 | if (sbrs.eq.'nh1 ') cgty='n'//res
|
|---|
| 682 | if (sbrs.eq.'nh2+') cgty='+'//res
|
|---|
| 683 | else
|
|---|
| 684 | if (sbrs.eq.'nh2 ') cgty='n'//res
|
|---|
| 685 | if (sbrs.eq.'nh3+') cgty='+'//res
|
|---|
| 686 | endif
|
|---|
| 687 | elseif (rpat.eq.'c '.and.nrs.eq.ilars) then
|
|---|
| 688 | if (sbrs.eq.'cooh') cgty='c'//res
|
|---|
| 689 | if (sbrs.eq.'coo-') cgty='-'//res
|
|---|
| 690 | else
|
|---|
| 691 | goto 10
|
|---|
| 692 | endif
|
|---|
| 693 | else
|
|---|
| 694 | write(logString,*)
|
|---|
| 695 | & ' redchg> dont know which end goup is present'
|
|---|
| 696 | stop
|
|---|
| 697 | endif
|
|---|
| 698 | ilib=1
|
|---|
| 699 | else
|
|---|
| 700 | cgty(1:)=sbrs
|
|---|
| 701 | ilib=2
|
|---|
| 702 | endif
|
|---|
| 703 |
|
|---|
| 704 | if (ilib.eq.1) then
|
|---|
| 705 |
|
|---|
| 706 | if (iopfil(lunchg,chgfil,'old','formatted').le.izero) then
|
|---|
| 707 | write (logString, '(a,/,a,i3,2a)')
|
|---|
| 708 | & ' redchg> ERROR opening library of charges:',
|
|---|
| 709 | & ' LUN=',lunchg,' FILE=',chgfil(1:iendst(chgfil))
|
|---|
| 710 | stop
|
|---|
| 711 | endif
|
|---|
| 712 |
|
|---|
| 713 | 1 line=' '
|
|---|
| 714 | read (lunchg,'(a)',end=3) line
|
|---|
| 715 | l=iendst(line)
|
|---|
| 716 |
|
|---|
| 717 | if (l.ge.10.and.line(1:1).eq.'#'.and.line(2:6).eq.cgty) then
|
|---|
| 718 | read (line(7:10),'(i4)') nchg
|
|---|
| 719 | if (nchg.le.mxath) then
|
|---|
| 720 | read (lunchg,'(10(2x,a4,1x))') (nmath(i),i=1,nchg)
|
|---|
| 721 | read (lunchg,'(10(f6.4,1x))') (cgath(i),i=1,nchg)
|
|---|
| 722 | close(lunchg)
|
|---|
| 723 | do i=iatrs1(nrs),iatrs2(nrs)
|
|---|
| 724 | atnm=nmat(i)
|
|---|
| 725 | do j=1,nchg
|
|---|
| 726 | if (nmath(j).eq.atnm) then
|
|---|
| 727 | cgat(i)=cgath(j)
|
|---|
| 728 | goto 2
|
|---|
| 729 | endif
|
|---|
| 730 | enddo
|
|---|
| 731 | write (logString, '(6a)') ' redchg> Cannot find atom: ',
|
|---|
| 732 | & atnm,
|
|---|
| 733 | & ' for entry: ',cgty,' in library: ',
|
|---|
| 734 | & chgfil(1:iendst(chgfil))
|
|---|
| 735 | stop
|
|---|
| 736 | 2 enddo
|
|---|
| 737 | return
|
|---|
| 738 | else
|
|---|
| 739 | write (logString, '(4a)')
|
|---|
| 740 | & ' redchg> must increase MXATH to read data for entry: ',
|
|---|
| 741 | & cgty,' in library: ',chgfil(1:iendst(chgfil))
|
|---|
| 742 | close(lunchg)
|
|---|
| 743 | stop
|
|---|
| 744 | endif
|
|---|
| 745 | endif
|
|---|
| 746 | goto 1
|
|---|
| 747 | 3 write (logString, '(4a)')
|
|---|
| 748 | & ' redchg> Cannot find entry: ',cgty,' in library: ',
|
|---|
| 749 | & chgfil(1:iendst(chgfil))
|
|---|
| 750 | close(lunchg)
|
|---|
| 751 | stop
|
|---|
| 752 |
|
|---|
| 753 | elseif (ilib.eq.2) then
|
|---|
| 754 |
|
|---|
| 755 | if (iopfil(lunlib,reslib,'old','formatted').le.izero) then
|
|---|
| 756 | write (logString, '(a,/,a,i3,2a)')
|
|---|
| 757 | & ' redchg> ERROR opening library of residues:',
|
|---|
| 758 | & ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib))
|
|---|
| 759 | stop
|
|---|
| 760 | endif
|
|---|
| 761 |
|
|---|
| 762 | 4 line=' '
|
|---|
| 763 | read (lunlib,'(a)',end=6) line
|
|---|
| 764 | l=iendst(line)
|
|---|
| 765 |
|
|---|
| 766 | if (l.ge.9.and.line(1:1).eq.'#'.and.line(2:5).eq.cgty(1:4)) then
|
|---|
| 767 | read (line(6:9),'(i4)') nchg
|
|---|
| 768 | if (nchg.le.mxath) then
|
|---|
| 769 | read (lunlib,'(a4,42x,d7.4)') (nmath(i),cgath(i),i=1,nchg)
|
|---|
| 770 | close(lunlib)
|
|---|
| 771 | do i=iatrs1(nrs),iatrs2(nrs)
|
|---|
| 772 | atnm=nmat(i)
|
|---|
| 773 | do j=1,nchg
|
|---|
| 774 | if (nmath(j).eq.atnm) then
|
|---|
| 775 | cgat(i)=cgath(j)
|
|---|
| 776 | goto 5
|
|---|
| 777 | endif
|
|---|
| 778 | enddo
|
|---|
| 779 | write (logString, '(6a)') ' redchg> Cannot find atom: ',
|
|---|
| 780 | & atnm,
|
|---|
| 781 | & ' for entry: ',cgty,' in library: ',
|
|---|
| 782 | & reslib(1:iendst(reslib))
|
|---|
| 783 | stop
|
|---|
| 784 | 5 enddo
|
|---|
| 785 | return
|
|---|
| 786 | else
|
|---|
| 787 | write (logString, '(4a)')
|
|---|
| 788 | & ' redchg> must increase MXATH to read data for entry: ',
|
|---|
| 789 | & cgty,' in library: ',reslib(1:iendst(reslib))
|
|---|
| 790 | close(lunchg)
|
|---|
| 791 | stop
|
|---|
| 792 | endif
|
|---|
| 793 | endif
|
|---|
| 794 | goto 4
|
|---|
| 795 | 6 write (logString, '(4a)')
|
|---|
| 796 | & ' redchg> Cannot find entry: ',cgty,' in library: ',
|
|---|
| 797 | & reslib(1:iendst(reslib))
|
|---|
| 798 | close(lunchg)
|
|---|
| 799 | stop
|
|---|
| 800 |
|
|---|
| 801 | endif
|
|---|
| 802 |
|
|---|
| 803 | 10 write (logString, '(4a)')
|
|---|
| 804 | & ' redchg> Do not have charges for N/C-terminal residue ',
|
|---|
| 805 | & res,' modified with group :',sbrs
|
|---|
| 806 | stop
|
|---|
| 807 |
|
|---|
| 808 | end
|
|---|
| 809 |
|
|---|
