| 1 | ! **************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: init_molecule
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| 4 | !
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| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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| 6 | ! Shura Hayryan, Chin-Ku
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| 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 8 | ! Jan H. Meinke, Sandipan Mohanty
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| 9 | !
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| 10 | ! **************************************************************
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| 11 | ! FIXME: Data in varfile determines which molecule is changed.
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| 12 |
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| 13 | subroutine init_molecule(iabin,grpn,grpc,seqfile,varfile)
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| 14 |
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| 15 | ! ----------------------------------------------------------
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| 16 | ! PURPOSE: construct starting structure of molecule(s)
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| 17 | !
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| 18 | ! iabin = 1 : ab Initio using sequence &
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| 19 | ! variables given in input files
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| 20 | ! iabin != 1 : sequence, variable information
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| 21 | ! from PDB-file
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| 22 | !
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| 23 | ! grpn: N-terminal group
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| 24 | ! grpc: C-terminal group
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| 25 | !
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| 26 | ! CALLS: addend,bldmol,c_alfa,getmol,iendst, mklist, nursvr,
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| 27 | ! pdbread,pdbvars,redseq,redvar,setmvs
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| 28 | !
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| 29 | ! ----------------------------------------------------------
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| 30 |
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| 31 | include 'INCL.H'
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| 32 | include 'INCP.H'
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| 33 |
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| 34 | !f2py character*80 optional, intent(in) :: seqfile = ' '
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| 35 | !f2py character*80 optional, intent(in) :: varfile = ' '
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| 36 |
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| 37 | character grpn*4,grpc*4
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| 38 | character navr*3, nars*4
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| 39 | character seqfile*80, varfile*80
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| 40 | integer ontlml
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| 41 | logical readFromStdin
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| 42 |
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| 43 | ontlml = 1
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| 44 | readFromStdin = .false.
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| 45 |
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| 46 | write (*,*) 'init_molecule: Solvent: ', itysol
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| 47 | if (iabin.eq.1) then
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| 48 |
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| 49 | ! ----------------------------------------- get sequence for molecule(s)
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| 50 | lunseq=11
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| 51 | if (ntlml.gt.0) then
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| 52 | ontlml = ntlml + 1
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| 53 | endif
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| 54 | if (iendst(seqfile).le.1.or.seqfile.eq.' ') then
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| 55 | 1 write (*,'(/,a,$)') ' file with SEQUENCE:'
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| 56 | seqfil=' '
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| 57 | read (*,'(a)',err=1) seqfil
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| 58 | readFromStdin = .true.
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| 59 | else
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| 60 | seqfil = seqfile
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| 61 | endif
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| 62 | call redseq
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| 63 |
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| 64 | write (*,*) 'File with sequence is ', seqfil(1:iendst(seqfil))
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| 65 |
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| 66 | ! --------------------------------- read & assemble data from libraries
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| 67 | ! initial coordinates, interaction lists
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| 68 |
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| 69 | ntl = ntlml
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| 70 | do i=ontlml, ntl
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| 71 |
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| 72 | call getmol(i) ! assemble data from libraries
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| 73 |
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| 74 | do j=1,6 ! initialize global parameters
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| 75 | gbpr(j,i)=0.d0
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| 76 | enddo
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| 77 |
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| 78 | call bldmol(i) ! co-ordinates
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| 79 |
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| 80 | ntlml = i
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| 81 | call addend(i,grpn,grpc) ! modify ends
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| 82 | call setmvs(i) ! determine sets of moving atoms for given variables
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| 83 | call mklist(i) ! compile lists of interaction partners
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| 84 |
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| 85 | enddo
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| 86 |
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| 87 | ! --------------------------- Read the initial conformation if necessary
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| 88 | if(readFromStdin) then
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| 89 | write (*,'(a,$)') ' file with VARIABLES:'
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| 90 | !
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| 91 | varfil=' '
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| 92 | read(*,'(a)',end=2,err=2) varfil
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| 93 | else
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| 94 | varfil = varfile
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| 95 | endif
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| 96 | l=iendst(varfil)
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| 97 | if (l.gt.0.and.varfil.ne.' ') then
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| 98 | write (*,'(1x,a,/)') varfil(1:l)
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| 99 | lunvar=13
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| 100 |
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| 101 | call redvar ! get vars. and rebuild
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| 102 |
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| 103 | endif
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| 104 |
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| 105 | 2 write(*,*) ' '
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| 106 |
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| 107 | ! If Lund force field is in use, keep omega angles fixed
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| 108 | if (ientyp.eq.2) then
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| 109 | do iv=1,nvrml(ntlml)
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| 110 | if (nmvr(iv).eq.'omg') then
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| 111 | print *, 'Fixed variable ',iv,nmvr(iv),vlvr(iv)
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| 112 | fxvr(iv)=.true.
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| 113 | endif
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| 114 | enddo
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| 115 | endif
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| 116 |
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| 117 | ! -------------------- get: nvr,idvr, vlvr, olvlvr
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| 118 | nvr = 0
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| 119 | do i=1,ivrml1(ntlml)+nvrml(ntlml)-1
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| 120 |
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| 121 | if (.not.fxvr(i)) then
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| 122 | nvr=nvr+1
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| 123 | idvr(nvr)=i ! index of not fixed var.
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| 124 | endif
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| 125 |
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| 126 | it=ityvr(i)
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| 127 |
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| 128 | if (it.eq.3) then ! torsion
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| 129 | vlvr(i)=toat(iatvr(i))
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| 130 | elseif (it.eq.2) then ! b.angle
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| 131 | vlvr(i)=baat(iatvr(i))
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| 132 | elseif (it.eq.1) then ! b.length
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| 133 | vlvr(i)=blat(iatvr(i))
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| 134 | endif
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| 135 |
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| 136 | olvlvr(i) = vlvr(i)
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| 137 | enddo
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| 138 |
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| 139 | ireg = 0
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| 140 |
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| 141 | else ! =========================== from PDB
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| 142 | if (iendst(seqfile).le.1) then
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| 143 | 3 write (*,'(/,a,$)') ' PDB-file:'
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| 144 | seqfil=' '
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| 145 | read (*,'(a)',err=3) seqfil
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| 146 | else
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| 147 | seqfil = seqfile
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| 148 | endif
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| 149 | write (*,*) 'PDB structure ',seqfil(1:iendst(seqfil))
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| 150 | print *, 'calling readpdb with ',seqfile
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| 151 | call pdbread(seqfil,ier)
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| 152 |
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| 153 | if (ier.ne.0) stop
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| 154 |
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| 155 | call pdbvars()
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| 156 |
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| 157 | ireg = 1
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| 158 |
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| 159 | endif
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| 160 |
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| 161 | ! -------------------------- set var. amplitudes for simulations
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| 162 |
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| 163 | do i=1,ivrml1(ntlml)+nvrml(ntlml)-1
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| 164 |
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| 165 | if (ityvr(i).eq.3.and..not.fxvr(i)) then ! torsion
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| 166 |
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| 167 | navr = nmvr(i)
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| 168 |
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| 169 | ir = nursvr(i)
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| 170 | nars = seq(ir)
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| 171 |
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| 172 | if ( navr(1:2).eq.'om'
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| 173 |
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| 174 | & .or.nars(1:3).eq.'arg'.and.(navr(1:2).eq.'x5'
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| 175 | & .or.navr(1:2).eq.'x6')
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| 176 |
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| 177 | & .or.(nars(1:3).eq.'asn'.or.nars(1:3).eq.'asp')
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| 178 | & .and.navr(1:2).eq.'x3'
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| 179 |
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| 180 | & .or.(nars(1:3).eq.'gln'.or.nars(1:3).eq.'glu')
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| 181 | & .and.navr(1:2).eq.'x4'
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| 182 |
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| 183 | & ) then
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| 184 |
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| 185 | ! axvr(i) = pi/9.d0 ! 20 deg.
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| 186 | axvr(i) = pi2 ! Trying out 360 deg. for these as well
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| 187 |
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| 188 | else
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| 189 | axvr(i) = pi2 ! 360 deg.
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| 190 | endif
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| 191 |
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| 192 | else
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| 193 | axvr(i) = 0.d0
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| 194 | endif
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| 195 |
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| 196 | enddo ! vars.
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| 197 |
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| 198 | ! --------------------- initialize solvation pars. if necessary
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| 199 |
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| 200 | if (itysol.ne.0) then
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| 201 |
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| 202 | i1=iatrs1(irsml1(1)) ! 1st atom of 1st molecule
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| 203 | i2=iatrs2(irsml2(ntlml)) ! last atom of last molecule
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| 204 |
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| 205 | its = iabs(itysol)
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| 206 |
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| 207 | do i=i1,i2 ! all atoms
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| 208 | it=ityat(i)
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| 209 | sigma(i)=coef_sl(its,it)
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| 210 | rvdw(i) =rad_vdw(its,it)
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| 211 |
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| 212 | if (nmat(i)(1:1).ne.'h') rvdw(i)=rvdw(i)+rwater
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| 213 |
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| 214 | enddo
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| 215 |
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| 216 | endif
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| 217 | ! Initialize calpha array
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| 218 | do i=ontlml, ntlml
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| 219 | call c_alfa(i,1)
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| 220 | enddo
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| 221 |
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| 222 | ! Initialize arrays used in the BGS update
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| 223 | call init_lund()
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| 224 | return
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| 225 | end
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| 226 |
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| 227 |
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