source/unres/io.f90

   1       module io
   2 !-----------------------------------------------------------------------
   3       use io_units
   4       use names
   5       use io_base
   6       use io_config
   7       implicit none
   8 !-----------------------------------------------------------------------------
   9 !
  10 !
  11 !-----------------------------------------------------------------------------
  12       contains
  13 !-----------------------------------------------------------------------------
  14 ! bank.F    io_csa
  15 !-----------------------------------------------------------------------------
  16       subroutine write_csa_pdb(var,ene,nft,ik,iw_pdb)
  17
  18       use csa_data
  19       use geometry_data, only:nres,nvar
  20       use geometry, only:var_to_geom,chainbuild
  21       use compare, only:secondary2
  22 !      implicit real*8 (a-h,o-z)
  23 !      include 'DIMENSIONS'
  24 !      include 'COMMON.CSA'
  25 !      include 'COMMON.BANK'
  26 !      include 'COMMON.VAR'
  27 !      include 'COMMON.IOUNITS'
  28 !      include 'COMMON.MINIM'
  29 !      include 'COMMON.SETUP'
  30 !      include 'COMMON.GEO'
  31 !      include 'COMMON.CHAIN'
  32 !      include 'COMMON.LOCAL'
  33 !      include 'COMMON.INTERACT'
  34 !      include 'COMMON.NAMES'
  35 !      include 'COMMON.SBRIDGE'
  36       integer :: lenpre,lenpot  !,ilen
  37 !el      external ilen
  38       real(kind=8),dimension(nvar) :: var       !(maxvar)       (maxvar=6*maxres)
  39       character(len=50) :: titelloc
  40       character(len=3) :: zahl
  41       real(kind=8),dimension(mxch*(mxch+1)/2+1) :: ene
  42 !el local variables
  43       integer :: nft,ik,iw_pdb
  44
  45       nmin_csa=nmin_csa+1
  46       if(ene(1).lt.eglob_csa) then
  47         eglob_csa=ene(1)
  48         nglob_csa=nglob_csa+1
  49         call numstr(nglob_csa,zahl)
  50
  51         call var_to_geom(nvar,var)
  52         call chainbuild
  53         call secondary2(.false.)
  54
  55         lenpre=ilen(prefix)
  56         open(icsa_pdb,file=prefix(:lenpre)//'@'//zahl//'.pdb')
  57
  58         if (iw_pdb.eq.1) then
  59           write(titelloc,'(a2,i3,a3,i9,a3,i6)') &
  60           'GM',nglob_csa,' e ',nft,' m ',nmin_csa
  61         else
  62           write(titelloc,'(a2,i3,a3,i9,a3,i6,a5,f5.2,a5,f5.1)') &
  63          'GM',nglob_csa,' e ',nft,' m ',nmin_csa,' rms ',&
  64                rmsn(ik),' %NC ',pncn(ik)*100
  65         endif
  66         call pdbout(eglob_csa,titelloc,icsa_pdb)
  67         close(icsa_pdb)
  68       endif
  69
  70       return
  71       end subroutine write_csa_pdb
  72 !-----------------------------------------------------------------------------
  73 ! csa.f         io_csa
  74 !-----------------------------------------------------------------------------
  75       subroutine from_pdb(n,idum)
  76 ! This subroutine stores the UNRES int variables generated from
  77 ! subroutine readpdb into the 1st conformation of in dihang_in.
  78 ! Subsequent n-1 conformations of dihang_in have identical values
  79 ! of theta and phi as the 1st conformation but random values for
  80 ! alph and omeg.
  81 ! The array cref (also generated from subroutine readpdb) is stored
  82 ! to crefjlee to be used for rmsd calculation in CSA, if necessary.
  83
  84       use csa_data
  85       use geometry_data
  86       use random, only: ran1
  87 !      implicit real*8 (a-h,o-z)
  88 !      include 'DIMENSIONS'
  89 !      include 'COMMON.IOUNITS'
  90 !      include 'COMMON.CHAIN'
  91 !      include 'COMMON.VAR'
  92 !      include 'COMMON.BANK'
  93 !      include 'COMMON.GEO'
  94 !el local variables
  95       integer :: n,idum,m,i,j,k,kk,kkk
  96       real(kind=8) :: e
  97
  98       m=1
  99       do j=2,nres-1
 100         dihang_in(1,j,1,m)=theta(j+1)
 101         dihang_in(2,j,1,m)=phi(j+2)
 102         dihang_in(3,j,1,m)=alph(j)
 103         dihang_in(4,j,1,m)=omeg(j)
 104       enddo
 105       dihang_in(2,nres-1,1,k)=0.0d0
 106
 107       do m=2,n
 108        do k=2,nres-1
 109         dihang_in(1,k,1,m)=dihang_in(1,k,1,1)
 110         dihang_in(2,k,1,m)=dihang_in(2,k,1,1)
 111         if(dabs(dihang_in(3,k,1,1)).gt.1.d-6) then
 112          dihang_in(3,k,1,m)=90.d0*ran1(idum)+90.d0
 113          dihang_in(3,k,1,m)=dihang_in(3,k,1,m)*deg2rad
 114         endif
 115         if(dabs(dihang_in(4,k,1,1)).gt.1.d-6) then
 116          dihang_in(4,k,1,m)=360.d0*ran1(idum)-180.d0
 117          dihang_in(4,k,1,m)=dihang_in(4,k,1,m)*deg2rad
 118         endif
 119        enddo
 120       enddo
 121
 122 ! Store cref to crefjlee (they are in COMMON.CHAIN).
 123       do k=1,2*nres
 124        do kk=1,3
 125         kkk=1
 126         crefjlee(kk,k)=cref(kk,k,kkk)
 127        enddo
 128       enddo
 129
 130       open(icsa_native_int,file=csa_native_int,status="old")
 131       do m=1,n
 132          write(icsa_native_int,*) m,e
 133          write(icsa_native_int,200) &
 134           (dihang_in(1,k,1,m)*rad2deg,k=2,nres-1)
 135          write(icsa_native_int,200) &
 136           (dihang_in(2,k,1,m)*rad2deg,k=2,nres-2)
 137          write(icsa_native_int,200) &
 138           (dihang_in(3,k,1,m)*rad2deg,k=2,nres-1)
 139          write(icsa_native_int,200) &
 140           (dihang_in(4,k,1,m)*rad2deg,k=2,nres-1)
 141       enddo
 142
 143       do k=1,nres
 144        write(icsa_native_int,200) (crefjlee(i,k),i=1,3)
 145       enddo
 146       close(icsa_native_int)
 147
 148   200 format (8f10.4)
 149
 150       return
 151       end subroutine from_pdb
 152 !-----------------------------------------------------------------------------
 153       subroutine from_int(n,mm,idum)
 154
 155       use csa_data
 156       use geometry_data
 157       use energy_data
 158       use geometry, only:chainbuild,gen_side
 159       use energy, only:etotal
 160       use compare
 161 !      implicit real*8 (a-h,o-z)
 162 !      include 'DIMENSIONS'
 163 !      include 'COMMON.IOUNITS'
 164 !      include 'COMMON.CHAIN'
 165 !      include 'COMMON.VAR'
 166 !      include 'COMMON.INTERACT'
 167 !      include 'COMMON.BANK'
 168 !      include 'COMMON.GEO'
 169 !      include 'COMMON.CONTACTS'
 170 !      integer ilen
 171 !el      external ilen
 172       logical :: fail
 173       real(kind=8),dimension(0:n_ene) :: energia
 174 !el local variables
 175       integer :: n,mm,idum,i,ii,j,m,k,kk,maxcount_fail,icount_fail,maxsi
 176       real(kind=8) :: co
 177
 178       open(icsa_native_int,file=csa_native_int,status="old")
 179       read (icsa_native_int,*)
 180       call read_angles(icsa_native_int,*10)
 181       goto 11
 182    10 write (iout,'(2a)') "CHUJ NASTAPIL - error in ",&
 183         csa_native_int(:ilen(csa_native_int))
 184    11 continue
 185       call intout
 186       do j=2,nres-1
 187         dihang_in(1,j,1,1)=theta(j+1)
 188         dihang_in(2,j,1,1)=phi(j+2)
 189         dihang_in(3,j,1,1)=alph(j)
 190         dihang_in(4,j,1,1)=omeg(j)
 191       enddo
 192       dihang_in(2,nres-1,1,1)=0.0d0
 193
 194 !         read(icsa_native_int,*) ind,e
 195 !         read(icsa_native_int,200) (dihang_in(1,k,1,1),k=2,nres-1)
 196 !         read(icsa_native_int,200) (dihang_in(2,k,1,1),k=2,nres-2)
 197 !         read(icsa_native_int,200) (dihang_in(3,k,1,1),k=2,nres-1)
 198 !         read(icsa_native_int,200) (dihang_in(4,k,1,1),k=2,nres-1)
 199 !         dihang_in(2,nres-1,1,1)=0.d0
 200
 201          maxsi=100
 202          maxcount_fail=100
 203
 204          do m=mm+2,n
 205 !          do k=2,nres-1
 206 !           dihang_in(1,k,1,m)=dihang_in(1,k,1,1)
 207 !           dihang_in(2,k,1,m)=dihang_in(2,k,1,1)
 208 !           if(abs(dihang_in(3,k,1,1)).gt.1.d-3) then
 209 !            dihang_in(3,k,1,m)=90.d0*ran1(idum)+90.d0
 210 !           endif
 211 !           if(abs(dihang_in(4,k,1,1)).gt.1.d-3) then
 212 !            dihang_in(4,k,1,m)=360.d0*ran1(idum)-180.d0
 213 !           endif
 214 !          enddo
 215 !           call intout
 216            fail=.true.
 217
 218            icount_fail=0
 219
 220            DO WHILE (FAIL .AND. ICOUNT_FAIL .LE. MAXCOUNT_FAIL)
 221
 222            do i=nnt,nct
 223              if (itype(i).ne.10) then
 224 !d             print *,'i=',i,' itype=',itype(i),' theta=',theta(i+1)
 225                fail=.true.
 226                ii=0
 227                do while (fail .and. ii .le. maxsi)
 228                  call gen_side(itype(i),theta(i+1),alph(i),omeg(i),fail)
 229                  ii = ii+1
 230                enddo
 231              endif
 232            enddo
 233            call chainbuild
 234            call etotal(energia)
 235            fail = (energia(0).ge.1.0d20)
 236            icount_fail=icount_fail+1
 237
 238            ENDDO
 239
 240            if (icount_fail.gt.maxcount_fail) then
 241              write (iout,*) &
 242              'Failed to generate non-overlaping near-native conf.',&
 243              m
 244            endif
 245
 246            do j=2,nres-1
 247              dihang_in(1,j,1,m)=theta(j+1)
 248              dihang_in(2,j,1,m)=phi(j+2)
 249              dihang_in(3,j,1,m)=alph(j)
 250              dihang_in(4,j,1,m)=omeg(j)
 251            enddo
 252            dihang_in(2,nres-1,1,m)=0.0d0
 253          enddo
 254
 255 !      do m=1,n
 256 !        write(icsa_native_int,*) m,e
 257 !         write(icsa_native_int,200) (dihang_in(1,k,1,m),k=2,nres-1)
 258 !         write(icsa_native_int,200) (dihang_in(2,k,1,m),k=2,nres-2)
 259 !         write(icsa_native_int,200) (dihang_in(3,k,1,m),k=2,nres-1)
 260 !         write(icsa_native_int,200) (dihang_in(4,k,1,m),k=2,nres-1)
 261 !      enddo
 262 !     close(icsa_native_int)
 263
 264 !      do m=mm+2,n
 265 !       do i=1,4
 266 !        do j=2,nres-1
 267 !         dihang_in(i,j,1,m)=dihang_in(i,j,1,m)*deg2rad
 268 !        enddo
 269 !       enddo
 270 !      enddo
 271
 272       call dihang_to_c(dihang_in(1,1,1,1))
 273
 274 ! Store c to cref (they are in COMMON.CHAIN).
 275       do k=1,2*nres
 276        do kk=1,3
 277         crefjlee(kk,k)=c(kk,k)
 278        enddo
 279       enddo
 280
 281       call contact(.true.,ncont_ref,icont_ref,co)
 282
 283 !      do k=1,nres
 284 !       write(icsa_native_int,200) (crefjlee(i,k),i=1,3)
 285 !      enddo
 286       close(icsa_native_int)
 287
 288   200 format (8f10.4)
 289
 290       return
 291       end subroutine from_int
 292 !-----------------------------------------------------------------------------
 293       subroutine dihang_to_c(aarray)
 294
 295       use geometry_data
 296       use csa_data
 297       use geometry, only:chainbuild
 298 !      implicit real*8 (a-h,o-z)
 299 !      include 'DIMENSIONS'
 300 !      include 'COMMON.CSA'
 301 !      include 'COMMON.BANK'
 302 !      include 'COMMON.CHAIN'
 303 !      include 'COMMON.GEO'
 304 !      include 'COMMON.VAR'
 305       integer :: i
 306       real(kind=8),dimension(mxang,nres,mxch) :: aarray !(mxang,maxres,mxch)
 307
 308 !     do i=4,nres
 309 !      phi(i)=dihang_in(1,i-2,1,1)
 310 !     enddo
 311       do i=2,nres-1
 312        theta(i+1)=aarray(1,i,1)
 313        phi(i+2)=aarray(2,i,1)
 314        alph(i)=aarray(3,i,1)
 315        omeg(i)=aarray(4,i,1)
 316       enddo
 317
 318       call chainbuild
 319
 320       return
 321       end subroutine dihang_to_c
 322 !-----------------------------------------------------------------------------
 323 ! geomout.F
 324 !-----------------------------------------------------------------------------
 325 #ifdef NOXDR
 326       subroutine cartout(time)
 327 #else
 328       subroutine cartoutx(time)
 329 #endif
 330       use geometry_data, only: c,nres
 331       use energy_data
 332       use MD_data, only: potE,t_bath
 333 !      implicit real*8 (a-h,o-z)
 334 !      include 'DIMENSIONS'
 335 !      include 'COMMON.CHAIN'
 336 !      include 'COMMON.INTERACT'
 337 !      include 'COMMON.NAMES'
 338 !      include 'COMMON.IOUNITS'
 339 !      include 'COMMON.HEADER'
 340 !      include 'COMMON.SBRIDGE'
 341 !      include 'COMMON.DISTFIT'
 342 !      include 'COMMON.MD'
 343       real(kind=8) :: time
 344 !el  local variables
 345       integer :: j,k,i
 346
 347 #if defined(AIX) || defined(PGI)
 348       open(icart,file=cartname,position="append")
 349 #else
 350       open(icart,file=cartname,access="append")
 351 #endif
 352       write (icart,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
 353       if (dyn_ss) then
 354        write (icart,'(i4,$)') &
 355          nss,(idssb(j)+nres,jdssb(j)+nres,j=1,nss)
 356       else
 357        write (icart,'(i4,$)') &
 358          nss,(ihpb(j),jhpb(j),j=1,nss)
 359        endif
 360        write (icart,'(i4,20f7.4)') nfrag+npair+3*nfrag_back,&
 361        (qfrag(i),i=1,nfrag),(qpair(i),i=1,npair),&
 362        (utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
 363       write (icart,'(8f10.5)') &
 364        ((c(k,j),k=1,3),j=1,nres),&
 365        ((c(k,j+nres),k=1,3),j=nnt,nct)
 366       close(icart)
 367       return
 368
 369 #ifdef NOXDR
 370       end subroutine cartout
 371 #else
 372       end subroutine cartoutx
 373 #endif
 374 !-----------------------------------------------------------------------------
 375 #ifndef NOXDR
 376       subroutine cartout(time)
 377 !      implicit real*8 (a-h,o-z)
 378 !      include 'DIMENSIONS'
 379       use geometry_data, only: c,nres
 380       use energy_data
 381       use MD_data, only: potE,t_bath
 382 #ifdef MPI
 383       use MPI_data
 384       include 'mpif.h'
 385 !      include 'COMMON.SETUP'
 386 #else
 387       integer,parameter :: me=0
 388 #endif
 389 !      include 'COMMON.CHAIN'
 390 !      include 'COMMON.INTERACT'
 391 !      include 'COMMON.NAMES'
 392 !      include 'COMMON.IOUNITS'
 393 !      include 'COMMON.HEADER'
 394 !      include 'COMMON.SBRIDGE'
 395 !      include 'COMMON.DISTFIT'
 396 !      include 'COMMON.MD'
 397       real(kind=8) :: time
 398       integer :: iret,itmp
 399       real(kind=4) :: prec
 400       real(kind=4),dimension(3,2*nres+2) :: xcoord      !(3,maxres2+2)  (maxres2=2*maxres
 401 !el  local variables
 402       integer :: j,i,ixdrf
 403
 404 #ifdef AIX
 405       call xdrfopen_(ixdrf,cartname, "a", iret)
 406       call xdrffloat_(ixdrf, real(time), iret)
 407       call xdrffloat_(ixdrf, real(potE), iret)
 408       call xdrffloat_(ixdrf, real(uconst), iret)
 409       call xdrffloat_(ixdrf, real(uconst_back), iret)
 410       call xdrffloat_(ixdrf, real(t_bath), iret)
 411       call xdrfint_(ixdrf, nss, iret)
 412       do j=1,nss
 413        if (dyn_ss) then
 414         call xdrfint_(ixdrf, idssb(j)+nres, iret)
 415         call xdrfint_(ixdrf, jdssb(j)+nres, iret)
 416        else
 417         call xdrfint_(ixdrf, ihpb(j), iret)
 418         call xdrfint_(ixdrf, jhpb(j), iret)
 419        endif
 420       enddo
 421       call xdrfint_(ixdrf, nfrag+npair+3*nfrag_back, iret)
 422       do i=1,nfrag
 423         call xdrffloat_(ixdrf, real(qfrag(i)), iret)
 424       enddo
 425       do i=1,npair
 426         call xdrffloat_(ixdrf, real(qpair(i)), iret)
 427       enddo
 428       do i=1,nfrag_back
 429         call xdrffloat_(ixdrf, real(utheta(i)), iret)
 430         call xdrffloat_(ixdrf, real(ugamma(i)), iret)
 431         call xdrffloat_(ixdrf, real(uscdiff(i)), iret)
 432       enddo
 433 #else
 434       call xdrfopen(ixdrf,cartname, "a", iret)
 435       call xdrffloat(ixdrf, real(time), iret)
 436       call xdrffloat(ixdrf, real(potE), iret)
 437       call xdrffloat(ixdrf, real(uconst), iret)
 438       call xdrffloat(ixdrf, real(uconst_back), iret)
 439       call xdrffloat(ixdrf, real(t_bath), iret)
 440       call xdrfint(ixdrf, nss, iret)
 441       do j=1,nss
 442        if (dyn_ss) then
 443         call xdrfint(ixdrf, idssb(j)+nres, iret)
 444         call xdrfint(ixdrf, jdssb(j)+nres, iret)
 445        else
 446         call xdrfint(ixdrf, ihpb(j), iret)
 447         call xdrfint(ixdrf, jhpb(j), iret)
 448        endif
 449       enddo
 450       call xdrfint(ixdrf, nfrag+npair+3*nfrag_back, iret)
 451       do i=1,nfrag
 452         call xdrffloat(ixdrf, real(qfrag(i)), iret)
 453       enddo
 454       do i=1,npair
 455         call xdrffloat(ixdrf, real(qpair(i)), iret)
 456       enddo
 457       do i=1,nfrag_back
 458         call xdrffloat(ixdrf, real(utheta(i)), iret)
 459         call xdrffloat(ixdrf, real(ugamma(i)), iret)
 460         call xdrffloat(ixdrf, real(uscdiff(i)), iret)
 461       enddo
 462 #endif
 463       prec=10000.0
 464       do i=1,nres
 465        do j=1,3
 466         xcoord(j,i)=c(j,i)
 467        enddo
 468       enddo
 469       do i=nnt,nct
 470        do j=1,3
 471         xcoord(j,nres+i-nnt+1)=c(j,i+nres)
 472        enddo
 473       enddo
 474
 475       itmp=nres+nct-nnt+1
 476 #ifdef AIX
 477       call xdrf3dfcoord_(ixdrf, xcoord, itmp, prec, iret)
 478       call xdrfclose_(ixdrf, iret)
 479 #else
 480       call xdrf3dfcoord(ixdrf, xcoord, itmp, prec, iret)
 481       call xdrfclose(ixdrf, iret)
 482 #endif
 483       return
 484       end subroutine cartout
 485 #endif
 486 !-----------------------------------------------------------------------------
 487       subroutine statout(itime)
 488
 489       use energy_data
 490       use control_data, only:refstr
 491       use MD_data
 492       use MPI_data
 493       use compare, only:rms_nac_nnc
 494 !      implicit real*8 (a-h,o-z)
 495 !      include 'DIMENSIONS'
 496 !      include 'COMMON.CONTROL'
 497 !      include 'COMMON.CHAIN'
 498 !      include 'COMMON.INTERACT'
 499 !      include 'COMMON.NAMES'
 500 !      include 'COMMON.IOUNITS'
 501 !      include 'COMMON.HEADER'
 502 !      include 'COMMON.SBRIDGE'
 503 !      include 'COMMON.DISTFIT'
 504 !      include 'COMMON.MD'
 505 !      include 'COMMON.REMD'
 506 !      include 'COMMON.SETUP'
 507       integer :: itime
 508       real(kind=8),dimension(0:n_ene) :: energia
 509 !      double precision gyrate
 510 !el      external gyrate
 511 !el      common /gucio/ cm
 512       character(len=256) :: line1,line2
 513       character(len=4) :: format1,format2
 514       character(len=30) :: format
 515 !el  local variables
 516       integer :: i,ii1,ii2
 517       real(kind=8) :: rms,frac,frac_nn,co
 518
 519 #ifdef AIX
 520       if(itime.eq.0) then
 521        open(istat,file=statname,position="append")
 522       endif
 523 #else
 524 #ifdef PGI
 525       open(istat,file=statname,position="append")
 526 #else
 527       open(istat,file=statname,access="append")
 528 #endif
 529 #endif
 530        if (refstr) then
 531          call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
 532           write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)') &
 533                 itime,totT,EK,potE,totE,&
 534                 rms,frac,frac_nn,co,amax,kinetic_T,t_bath,gyrate(),me
 535           format1="a133"
 536         else
 537           write (line1,'(i10,f15.2,7f12.3,i5,$)') &
 538                  itime,totT,EK,potE,totE,&
 539                  amax,kinetic_T,t_bath,gyrate(),me
 540           format1="a114"
 541         endif
 542         if(usampl.and.totT.gt.eq_time) then
 543            write(line2,'(i5,2f9.4,300f7.4)') iset,uconst,uconst_back,&
 544             (qfrag(ii1),ii1=1,nfrag),(qpair(ii2),ii2=1,npair),&
 545             (utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
 546            write(format2,'(a1,i3.3)') "a",23+7*nfrag+7*npair &
 547                    +21*nfrag_back
 548         else
 549            format2="a001"
 550            line2=' '
 551         endif
 552         if (print_compon) then
 553           if(itime.eq.0) then
 554            write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,&
 555                                                            ",20a12)"
 556            write (istat,format) "#","",&
 557             (ename(print_order(i)),i=1,nprint_ene)
 558           endif
 559           write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,&
 560                                                            ",20f12.3)"
 561           write (istat,format) line1,line2,&
 562             (potEcomp(print_order(i)),i=1,nprint_ene)
 563         else
 564           write(format,'(a1,a4,a1,a4,a1)') "(",format1,",",format2,")"
 565           write (istat,format) line1,line2
 566         endif
 567 #if defined(AIX)
 568         call flush(istat)
 569 #else
 570         close(istat)
 571 #endif
 572       return
 573       end subroutine  statout
 574 !-----------------------------------------------------------------------------
 575 ! readrtns_CSA.F
 576 !-----------------------------------------------------------------------------
 577       subroutine readrtns
 578
 579       use control_data
 580       use energy_data
 581       use MPI_data
 582       use muca_md, only:read_muca
 583 !      implicit real*8 (a-h,o-z)
 584 !      include 'DIMENSIONS'
 585 #ifdef MPI
 586       include 'mpif.h'
 587 #endif
 588 !      include 'COMMON.SETUP'
 589 !      include 'COMMON.CONTROL'
 590 !      include 'COMMON.SBRIDGE'
 591 !      include 'COMMON.IOUNITS'
 592       logical :: file_exist
 593       integer :: i
 594 ! Read force-field parameters except weights
 595       call parmread
 596 ! Read job setup parameters
 597       call read_control
 598 ! Read control parameters for energy minimzation if required
 599       if (minim) call read_minim
 600 ! Read MCM control parameters if required
 601       if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
 602 ! Read MD control parameters if reqjuired
 603       if (modecalc.eq.12) call read_MDpar
 604 ! Read MREMD control parameters if required
 605       if (modecalc.eq.14) then
 606          call read_MDpar
 607          call read_REMDpar
 608       endif
 609 ! Read MUCA control parameters if required
 610       if (lmuca) call read_muca
 611 ! Read CSA control parameters if required (from fort.40 if exists
 612 ! otherwise from general input file)
 613       if (modecalc.eq.8) then
 614        inquire (file="fort.40",exist=file_exist)
 615        if (.not.file_exist) call csaread
 616       endif
 617 !fmc      if (modecalc.eq.10) call mcmfread
 618 ! Read molecule information, molecule geometry, energy-term weights, and
 619 ! restraints if requested
 620       call molread
 621 ! Print restraint information
 622 #ifdef MPI
 623       if (.not. out1file .or. me.eq.king) then
 624 #endif
 625       if (nhpb.gt.nss) &
 626       write (iout,'(a,i5,a)') "The following",nhpb-nss,&
 627        " distance constraints have been imposed"
 628       do i=nss+1,nhpb
 629         write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
 630       enddo
 631 #ifdef MPI
 632       endif
 633 #endif
 634 !      print *,"Processor",myrank," leaves READRTNS"
 635 !      write(iout,*) "end readrtns"
 636       return
 637       end subroutine readrtns
 638 !-----------------------------------------------------------------------------
 639       subroutine molread
 640 !
 641 ! Read molecular data.
 642 !
 643 !      use control, only: ilen
 644       use control_data
 645       use geometry_data
 646       use energy_data
 647       use energy
 648       use compare_data
 649       use MD_data, only: t_bath
 650       use MPI_data
 651       use compare, only:seq_comp,contact
 652       use control
 653 !      implicit real*8 (a-h,o-z)
 654 !      include 'DIMENSIONS'
 655 #ifdef MPI
 656       include 'mpif.h'
 657       integer :: error_msg,ierror,ierr,ierrcode
 658 #endif
 659 !      include 'COMMON.IOUNITS'
 660 !      include 'COMMON.GEO'
 661 !      include 'COMMON.VAR'
 662 !      include 'COMMON.INTERACT'
 663 !      include 'COMMON.LOCAL'
 664 !      include 'COMMON.NAMES'
 665 !      include 'COMMON.CHAIN'
 666 !      include 'COMMON.FFIELD'
 667 !      include 'COMMON.SBRIDGE'
 668 !      include 'COMMON.HEADER'
 669 !      include 'COMMON.CONTROL'
 670 !      include 'COMMON.DBASE'
 671 !      include 'COMMON.THREAD'
 672 !      include 'COMMON.CONTACTS'
 673 !      include 'COMMON.TORCNSTR'
 674 !      include 'COMMON.TIME1'
 675 !      include 'COMMON.BOUNDS'
 676 !      include 'COMMON.MD'
 677 !      include 'COMMON.SETUP'
 678       character(len=4),dimension(:),allocatable :: sequence     !(maxres)
 679 !      integer :: rescode
 680 !      double precision x(maxvar)
 681       character(len=256) :: pdbfile
 682       character(len=320) :: weightcard
 683       character(len=80) :: weightcard_t!,ucase
 684 !      integer,dimension(:),allocatable :: itype_pdb    !(maxres)
 685 !      common /pizda/ itype_pdb
 686       logical :: fail   !seq_comp,
 687       real(kind=8) :: energia(0:n_ene)
 688 !      integer ilen
 689 !el      external ilen
 690 !el local varables
 691       integer :: i,j,l,k,kkk,ii,i1,i2,it1,it2
 692
 693       real(kind=8),dimension(3,maxres2+2) :: c_alloc
 694       real(kind=8),dimension(3,0:maxres2) :: dc_alloc
 695       integer,dimension(maxres) :: itype_alloc
 696
 697       integer :: iti,nsi,maxsi,itrial,itmp
 698       real(kind=8) :: wlong,scalscp,co
 699       allocate(weights(n_ene))
 700 !-----------------------------
 701       allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres
 702       allocate(dc(3,0:2*maxres)) !(3,0:maxres2)
 703       allocate(itype(maxres)) !(maxres)
 704 !
 705 ! Zero out tables.
 706 !
 707       do i=1,2*maxres
 708         do j=1,3
 709           c(j,i)=0.0D0
 710           dc(j,i)=0.0D0
 711         enddo
 712       enddo
 713       do i=1,maxres
 714          itype(i)=0
 715       enddo
 716 !-----------------------------
 717 !
 718 ! Body
 719 !
 720 ! Read weights of the subsequent energy terms.
 721       call card_concat(weightcard,.true.)
 722       call reada(weightcard,'WLONG',wlong,1.0D0)
 723       call reada(weightcard,'WSC',wsc,wlong)
 724       call reada(weightcard,'WSCP',wscp,wlong)
 725       call reada(weightcard,'WELEC',welec,1.0D0)
 726       call reada(weightcard,'WVDWPP',wvdwpp,welec)
 727       call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 728       call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 729       call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 730       call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 731       call reada(weightcard,'WTURN3',wturn3,1.0D0)
 732       call reada(weightcard,'WTURN4',wturn4,1.0D0)
 733       call reada(weightcard,'WTURN6',wturn6,1.0D0)
 734       call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 735       call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 736       call reada(weightcard,'WBOND',wbond,1.0D0)
 737       call reada(weightcard,'WTOR',wtor,1.0D0)
 738       call reada(weightcard,'WTORD',wtor_d,1.0D0)
 739       call reada(weightcard,'WANG',wang,1.0D0)
 740       call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 741       call reada(weightcard,'SCAL14',scal14,0.4D0)
 742       call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 743       call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 744       call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 745       call reada(weightcard,'TEMP0',temp0,300.0d0)
 746       if (index(weightcard,'SOFT').gt.0) ipot=6
 747 ! 12/1/95 Added weight for the multi-body term WCORR
 748       call reada(weightcard,'WCORRH',wcorr,1.0D0)
 749       if (wcorr4.gt.0.0d0) wcorr=wcorr4
 750       weights(1)=wsc
 751       weights(2)=wscp
 752       weights(3)=welec
 753       weights(4)=wcorr
 754       weights(5)=wcorr5
 755       weights(6)=wcorr6
 756       weights(7)=wel_loc
 757       weights(8)=wturn3
 758       weights(9)=wturn4
 759       weights(10)=wturn6
 760       weights(11)=wang
 761       weights(12)=wscloc
 762       weights(13)=wtor
 763       weights(14)=wtor_d
 764       weights(15)=wstrain
 765       weights(16)=wvdwpp
 766       weights(17)=wbond
 767       weights(18)=scal14
 768       weights(21)=wsccor
 769       if(me.eq.king.or..not.out1file) &
 770        write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
 771         wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
 772         wturn4,wturn6
 773    10 format (/'Energy-term weights (unscaled):'// &
 774        'WSCC=   ',f10.6,' (SC-SC)'/ &
 775        'WSCP=   ',f10.6,' (SC-p)'/ &
 776        'WELEC=  ',f10.6,' (p-p electr)'/ &
 777        'WVDWPP= ',f10.6,' (p-p VDW)'/ &
 778        'WBOND=  ',f10.6,' (stretching)'/ &
 779        'WANG=   ',f10.6,' (bending)'/ &
 780        'WSCLOC= ',f10.6,' (SC local)'/ &
 781        'WTOR=   ',f10.6,' (torsional)'/ &
 782        'WTORD=  ',f10.6,' (double torsional)'/ &
 783        'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
 784        'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
 785        'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
 786        'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
 787        'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
 788        'WSCCOR= ',f10.6,' (back-scloc correlation)'/ &
 789        'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
 790        'WTURN4= ',f10.6,' (turns, 4th order)'/ &
 791        'WTURN6= ',f10.6,' (turns, 6th order)')
 792       if(me.eq.king.or..not.out1file)then
 793        if (wcorr4.gt.0.0d0) then
 794         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',&
 795          'between contact pairs of peptide groups'
 796         write (iout,'(2(a,f5.3/))') &
 797         'Cutoff on 4-6th order correlation terms: ',cutoff_corr,&
 798         'Range of quenching the correlation terms:',2*delt_corr
 799        else if (wcorr.gt.0.0d0) then
 800         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',&
 801          'between contact pairs of peptide groups'
 802        endif
 803        write (iout,'(a,f8.3)') &
 804         'Scaling factor of 1,4 SC-p interactions:',scal14
 805        write (iout,'(a,f8.3)') &
 806         'General scaling factor of SC-p interactions:',scalscp
 807       endif
 808       r0_corr=cutoff_corr-delt_corr
 809       do i=1,ntyp
 810         aad(i,1)=scalscp*aad(i,1)
 811         aad(i,2)=scalscp*aad(i,2)
 812         bad(i,1)=scalscp*bad(i,1)
 813         bad(i,2)=scalscp*bad(i,2)
 814       enddo
 815       call rescale_weights(t_bath)
 816       if(me.eq.king.or..not.out1file) &
 817        write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
 818         wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
 819         wturn4,wturn6
 820    22 format (/'Energy-term weights (scaled):'// &
 821        'WSCC=   ',f10.6,' (SC-SC)'/ &
 822        'WSCP=   ',f10.6,' (SC-p)'/ &
 823        'WELEC=  ',f10.6,' (p-p electr)'/ &
 824        'WVDWPP= ',f10.6,' (p-p VDW)'/ &
 825        'WBOND=  ',f10.6,' (stretching)'/ &
 826        'WANG=   ',f10.6,' (bending)'/ &
 827        'WSCLOC= ',f10.6,' (SC local)'/ &
 828        'WTOR=   ',f10.6,' (torsional)'/ &
 829        'WTORD=  ',f10.6,' (double torsional)'/ &
 830        'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
 831        'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
 832        'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
 833        'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
 834        'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
 835        'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/ &
 836        'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
 837        'WTURN4= ',f10.6,' (turns, 4th order)'/ &
 838        'WTURN6= ',f10.6,' (turns, 6th order)')
 839       if(me.eq.king.or..not.out1file) &
 840        write (iout,*) "Reference temperature for weights calculation:",&
 841         temp0
 842       call reada(weightcard,"D0CM",d0cm,3.78d0)
 843       call reada(weightcard,"AKCM",akcm,15.1d0)
 844       call reada(weightcard,"AKTH",akth,11.0d0)
 845       call reada(weightcard,"AKCT",akct,12.0d0)
 846       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 847       call reada(weightcard,"V2SS",v2ss,7.61d0)
 848       call reada(weightcard,"V3SS",v3ss,13.7d0)
 849       call reada(weightcard,"EBR",ebr,-5.50D0)
 850       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 851
 852       call reada(weightcard,"HT",Ht,0.0D0)
 853       if (dyn_ss) then
 854         ss_depth=ebr/wsc-0.25*eps(1,1)
 855         Ht=Ht/wsc-0.25*eps(1,1)
 856         akcm=akcm*wstrain/wsc
 857         akth=akth*wstrain/wsc
 858         akct=akct*wstrain/wsc
 859         v1ss=v1ss*wstrain/wsc
 860         v2ss=v2ss*wstrain/wsc
 861         v3ss=v3ss*wstrain/wsc
 862       else
 863         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 864       endif
 865
 866       if(me.eq.king.or..not.out1file) then
 867        write (iout,*) "Parameters of the SS-bond potential:"
 868        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,&
 869        " AKCT",akct
 870        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 871        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 872        write (iout,*)" HT",Ht
 873        print *,'indpdb=',indpdb,' pdbref=',pdbref
 874       endif
 875       if (indpdb.gt.0 .or. pdbref) then
 876         read(inp,'(a)') pdbfile
 877         if(me.eq.king.or..not.out1file) &
 878          write (iout,'(2a)') 'PDB data will be read from file ',&
 879          pdbfile(:ilen(pdbfile))
 880         open(ipdbin,file=pdbfile,status='old',err=33)
 881         goto 34
 882   33    write (iout,'(a)') 'Error opening PDB file.'
 883         stop
 884   34    continue
 885 !        print *,'Begin reading pdb data'
 886         call readpdb
 887 !        print *,'Finished reading pdb data'
 888         if(me.eq.king.or..not.out1file) &
 889          write (iout,'(a,i3,a,i3)')'nsup=',nsup,&
 890          ' nstart_sup=',nstart_sup !,"ergwergewrgae"
 891 !el        if(.not.allocated(itype_pdb))
 892         allocate(itype_pdb(nres))
 893         do i=1,nres
 894           itype_pdb(i)=itype(i)
 895         enddo
 896         close (ipdbin)
 897         nnt=nstart_sup
 898         nct=nstart_sup+nsup-1
 899 !el        if(.not.allocated(icont_ref))
 900         allocate(icont_ref(2,12*nres)) ! maxcont=12*maxres
 901         call contact(.false.,ncont_ref,icont_ref,co)
 902
 903         if (sideadd) then
 904          if(me.eq.king.or..not.out1file) &
 905           write(iout,*)'Adding sidechains'
 906          maxsi=1000
 907          do i=2,nres-1
 908           iti=itype(i)
 909           if (iti.ne.10 .and. itype(i).ne.ntyp1) then
 910             nsi=0
 911             fail=.true.
 912             do while (fail.and.nsi.le.maxsi)
 913               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
 914               nsi=nsi+1
 915             enddo
 916             if(fail) write(iout,*)'Adding sidechain failed for res ',&
 917                     i,' after ',nsi,' trials'
 918           endif
 919          enddo
 920         endif
 921       endif
 922
 923       if (indpdb.eq.0) then
 924 ! Read sequence if not taken from the pdb file.
 925         read (inp,*) nres
 926 !        print *,'nres=',nres
 927         allocate(sequence(nres))
 928         if (iscode.gt.0) then
 929           read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
 930         else
 931           read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
 932         endif
 933 ! Convert sequence to numeric code
 934         do i=1,nres
 935           itype(i)=rescode(i,sequence(i),iscode)
 936         enddo
 937 ! Assign initial virtual bond lengths
 938 !elwrite(iout,*) "test_alloc"
 939         if(.not.allocated(vbld)) allocate(vbld(2*nres))
 940 !elwrite(iout,*) "test_alloc"
 941         if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
 942 !elwrite(iout,*) "test_alloc"
 943         do i=2,nres
 944           vbld(i)=vbl
 945           vbld_inv(i)=vblinv
 946         enddo
 947         do i=2,nres-1
 948           vbld(i+nres)=dsc(iabs(itype(i)))
 949           vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
 950 !          write (iout,*) "i",i," itype",itype(i),
 951 !     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
 952         enddo
 953       endif
 954 !      print *,nres
 955 !      print '(20i4)',(itype(i),i=1,nres)
 956 !----------------------------
 957 !el reallocate tables
 958 !      do i=1,maxres2
 959 !        do j=1,3
 960 !          c_alloc(j,i)=c(j,i)
 961 !          dc_alloc(j,i)=dc(j,i)
 962 !        enddo
 963 !      enddo
 964 !      do i=1,maxres
 965 !elwrite(iout,*) "itype",i,itype(i)
 966 !        itype_alloc(i)=itype(i)
 967 !      enddo
 968
 969 !      deallocate(c)
 970 !      deallocate(dc)
 971 !      deallocate(itype)
 972 !      allocate(c(3,2*nres+4))
 973 !      allocate(dc(3,0:2*nres+2))
 974 !      allocate(itype(nres+2))
 975       allocate(itel(nres+2))
 976
 977 !      do i=1,2*nres+2
 978 !        do j=1,3
 979 !          c(j,i)=c_alloc(j,i)
 980 !          dc(j,i)=dc_alloc(j,i)
 981 !        enddo
 982 !      enddo
 983       do i=1,nres+2
 984 !        itype(i)=itype_alloc(i)
 985         itel(i)=0
 986       enddo
 987 !--------------------------
 988       do i=1,nres
 989 #ifdef PROCOR
 990         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
 991 #else
 992         if (itype(i).eq.ntyp1) then
 993 #endif
 994           itel(i)=0
 995 #ifdef PROCOR
 996         else if (iabs(itype(i+1)).ne.20) then
 997 #else
 998         else if (iabs(itype(i)).ne.20) then
 999 #endif
1000           itel(i)=1
1001         else
1002           itel(i)=2
1003         endif
1004       enddo
1005       if(me.eq.king.or..not.out1file)then
1006        write (iout,*) "ITEL"
1007        do i=1,nres-1
1008          write (iout,*) i,itype(i),itel(i)
1009        enddo
1010        print *,'Call Read_Bridge.'
1011       endif
1012       call read_bridge
1013 !--------------------------------
1014 ! znamy nres oraz nss można zaalokowac potrzebne tablice
1015       call alloc_geo_arrays
1016       call alloc_ener_arrays
1017 !--------------------------------
1018 ! 8/13/98 Set limits to generating the dihedral angles
1019       do i=1,nres
1020         phibound(1,i)=-pi
1021         phibound(2,i)=pi
1022       enddo
1023       read (inp,*) ndih_constr
1024       if (ndih_constr.gt.0) then
1025         allocate(idih_constr(ndih_constr),idih_nconstr(ndih_constr)) !(maxdih_constr)
1026         allocate(phi0(ndih_constr),drange(ndih_constr)) !(maxdih_constr)
1027         read (inp,*) ftors
1028         read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
1029         if(me.eq.king.or..not.out1file)then
1030          write (iout,*) &
1031          'There are',ndih_constr,' constraints on phi angles.'
1032          do i=1,ndih_constr
1033           write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
1034          enddo
1035         endif
1036         do i=1,ndih_constr
1037           phi0(i)=deg2rad*phi0(i)
1038           drange(i)=deg2rad*drange(i)
1039         enddo
1040         if(me.eq.king.or..not.out1file) &
1041          write (iout,*) 'FTORS',ftors
1042         do i=1,ndih_constr
1043           ii = idih_constr(i)
1044           phibound(1,ii) = phi0(i)-drange(i)
1045           phibound(2,ii) = phi0(i)+drange(i)
1046         enddo
1047       endif
1048       nnt=1
1049 #ifdef MPI
1050       if (me.eq.king) then
1051 #endif
1052        write (iout,'(a)') 'Boundaries in phi angle sampling:'
1053        do i=1,nres
1054          write (iout,'(a3,i5,2f10.1)') &
1055          restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1056        enddo
1057 #ifdef MP
1058       endif
1059 #endif
1060       nct=nres
1061 !d      print *,'NNT=',NNT,' NCT=',NCT
1062       if (itype(1).eq.ntyp1) nnt=2
1063       if (itype(nres).eq.ntyp1) nct=nct-1
1064       if (pdbref) then
1065         if(me.eq.king.or..not.out1file) &
1066          write (iout,'(a,i3)') 'nsup=',nsup
1067         nstart_seq=nnt
1068         if (nsup.le.(nct-nnt+1)) then
1069           do i=0,nct-nnt+1-nsup
1070             if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
1071               nstart_seq=nnt+i
1072               goto 111
1073             endif
1074           enddo
1075           write (iout,'(a)') &
1076                   'Error - sequences to be superposed do not match.'
1077           stop
1078         else
1079           do i=0,nsup-(nct-nnt+1)
1080             if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1)) &
1081             then
1082               nstart_sup=nstart_sup+i
1083               nsup=nct-nnt+1
1084               goto 111
1085             endif
1086           enddo
1087           write (iout,'(a)') &
1088                   'Error - sequences to be superposed do not match.'
1089         endif
1090   111   continue
1091         if (nsup.eq.0) nsup=nct-nnt
1092         if (nstart_sup.eq.0) nstart_sup=nnt
1093         if (nstart_seq.eq.0) nstart_seq=nnt
1094         if(me.eq.king.or..not.out1file) &
1095          write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,&
1096                        ' nstart_seq=',nstart_seq !,"242343453254"
1097       endif
1098 !--- Zscore rms -------
1099       if (nz_start.eq.0) nz_start=nnt
1100       if (nz_end.eq.0 .and. nsup.gt.0) then
1101         nz_end=nnt+nsup-1
1102       else if (nz_end.eq.0) then
1103         nz_end=nct
1104       endif
1105       if(me.eq.king.or..not.out1file)then
1106        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1107        write (iout,*) 'IZ_SC=',iz_sc
1108       endif
1109 !----------------------
1110       call init_int_table
1111       if (refstr) then
1112         if (.not.pdbref) then
1113           call read_angles(inp,*38)
1114           goto 39
1115    38     write (iout,'(a)') 'Error reading reference structure.'
1116 #ifdef MPI
1117           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1118           stop 'Error reading reference structure'
1119 #endif
1120    39     call chainbuild
1121           call setup_var
1122 !zscore          call geom_to_var(nvar,coord_exp_zs(1,1))
1123           nstart_sup=nnt
1124           nstart_seq=nnt
1125           nsup=nct-nnt+1
1126           kkk=1
1127           do i=1,2*nres
1128             do j=1,3
1129               cref(j,i,kkk)=c(j,i)
1130             enddo
1131           enddo
1132           call contact(.true.,ncont_ref,icont_ref,co)
1133         endif
1134 !        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1135         call flush(iout)
1136         if (constr_dist.gt.0) call read_dist_constr
1137         write (iout,*) "After read_dist_constr nhpb",nhpb
1138         call hpb_partition
1139         if(me.eq.king.or..not.out1file) &
1140          write (iout,*) 'Contact order:',co
1141         if (pdbref) then
1142         if(me.eq.king.or..not.out1file) &
1143          write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1144         do i=1,ncont_ref
1145           do j=1,2
1146             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1147           enddo
1148           if(me.eq.king.or..not.out1file) &
1149            write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',&
1150            icont_ref(1,i),' ',&
1151            restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
1152         enddo
1153         endif
1154       endif
1155       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 &
1156           .and. modecalc.ne.8 .and. modecalc.ne.9 .and. &
1157           modecalc.ne.10) then
1158 ! If input structure hasn't been supplied from the PDB file read or generate
1159 ! initial geometry.
1160         if (iranconf.eq.0 .and. .not. extconf) then
1161           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) &
1162            write (iout,'(a)') 'Initial geometry will be read in.'
1163           if (read_cart) then
1164             read(inp,'(8f10.5)',end=36,err=36) &
1165              ((c(l,k),l=1,3),k=1,nres),&
1166              ((c(l,k+nres),l=1,3),k=nnt,nct)
1167             write (iout,*) "Exit READ_CART"
1168             write (iout,'(8f10.5)') &
1169              ((c(l,k),l=1,3),k=1,nres),&
1170              ((c(l,k+nres),l=1,3),k=nnt,nct)
1171             call int_from_cart1(.true.)
1172             write (iout,*) "Finish INT_TO_CART"
1173             do i=1,nres-1
1174               do j=1,3
1175                 dc(j,i)=c(j,i+1)-c(j,i)
1176                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1177               enddo
1178             enddo
1179             do i=nnt,nct
1180               if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
1181                 do j=1,3
1182                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
1183                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1184                 enddo
1185               endif
1186             enddo
1187             return
1188           else
1189             call read_angles(inp,*36)
1190           endif
1191           goto 37
1192    36     write (iout,'(a)') 'Error reading angle file.'
1193 #ifdef MPI
1194           call mpi_finalize( MPI_COMM_WORLD,IERR )
1195 #endif
1196           stop 'Error reading angle file.'
1197    37     continue
1198         else if (extconf) then
1199          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0) &
1200           write (iout,'(a)') 'Extended chain initial geometry.'
1201          do i=3,nres
1202           theta(i)=90d0*deg2rad
1203          enddo
1204          do i=4,nres
1205           phi(i)=180d0*deg2rad
1206          enddo
1207          do i=2,nres-1
1208           alph(i)=110d0*deg2rad
1209          enddo
1210 !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
1211          do i=2,nres-1
1212           omeg(i)=-120d0*deg2rad
1213           if (itype(i).le.0) omeg(i)=-omeg(i)
1214          enddo
1215         else
1216           if(me.eq.king.or..not.out1file) &
1217            write (iout,'(a)') 'Random-generated initial geometry.'
1218
1219
1220 #ifdef MPI
1221           if (me.eq.king  .or. fg_rank.eq.0 .and. &
1222                  ( modecalc.eq.12 .or. modecalc.eq.14) ) then
1223 #endif
1224             do itrial=1,100
1225               itmp=1
1226               call gen_rand_conf(itmp,*30)
1227               goto 40
1228    30         write (iout,*) 'Failed to generate random conformation',&
1229                 ', itrial=',itrial
1230               write (*,*) 'Processor:',me,&
1231                 ' Failed to generate random conformation',&
1232                 ' itrial=',itrial
1233               call intout
1234
1235 #ifdef AIX
1236               call flush_(iout)
1237 #else
1238               call flush(iout)
1239 #endif
1240             enddo
1241             write (iout,'(a,i3,a)') 'Processor:',me,&
1242               ' error in generating random conformation.'
1243             write (*,'(a,i3,a)') 'Processor:',me,&
1244               ' error in generating random conformation.'
1245             call flush(iout)
1246 #ifdef MPI
1247             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1248    40       continue
1249           endif
1250 #else
1251           do itrial=1,100
1252             itmp=1
1253             call gen_rand_conf(itmp,*335)
1254             goto 40
1255   335       write (iout,*) 'Failed to generate random conformation',&
1256               ', itrial=',itrial
1257             write (*,*) 'Failed to generate random conformation',&
1258               ', itrial=',itrial
1259           enddo
1260           write (iout,'(a,i3,a)') 'Processor:',me,&
1261             ' error in generating random conformation.'
1262           write (*,'(a,i3,a)') 'Processor:',me,&
1263             ' error in generating random conformation.'
1264           stop
1265    40     continue
1266 #endif
1267         endif
1268       elseif (modecalc.eq.4) then
1269         read (inp,'(a)') intinname
1270         open (intin,file=intinname,status='old',err=333)
1271         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0) &
1272         write (iout,'(a)') 'intinname',intinname
1273         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1274         goto 334
1275   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1276 #ifdef MPI
1277         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1278 #endif
1279         stop 'Error opening angle file.'
1280   334   continue
1281
1282       endif
1283 ! Generate distance constraints, if the PDB structure is to be regularized.
1284       if (nthread.gt.0) then
1285         call read_threadbase
1286       endif
1287       call setup_var
1288 !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
1289       if (me.eq.king .or. .not. out1file) &
1290        call intout
1291 !elwrite (iout,*)"alph(i)*rad2deg",(alph(i)*rad2deg, i=1,nres)
1292       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1293         write (iout,'(/a,i3,a)') &
1294         'The chain contains',ns,' disulfide-bridging cysteines.'
1295         write (iout,'(20i4)') (iss(i),i=1,ns)
1296        if (dyn_ss) then
1297           write(iout,*)"Running with dynamic disulfide-bond formation"
1298        else
1299         write (iout,'(/a/)') 'Pre-formed links are:'
1300         do i=1,nss
1301           i1=ihpb(i)-nres
1302           i2=jhpb(i)-nres
1303           it1=itype(i1)
1304           it2=itype(i2)
1305           if (me.eq.king.or..not.out1file) &
1306           write (iout,'(2a,i3,3a,i3,a,3f10.3)') &
1307           restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),&
1308           ebr,forcon(i)
1309         enddo
1310         write (iout,'(a)')
1311        endif
1312       endif
1313       if (ns.gt.0.and.dyn_ss) then
1314           do i=nss+1,nhpb
1315             ihpb(i-nss)=ihpb(i)
1316             jhpb(i-nss)=jhpb(i)
1317             forcon(i-nss)=forcon(i)
1318             dhpb(i-nss)=dhpb(i)
1319           enddo
1320           nhpb=nhpb-nss
1321           nss=0
1322           call hpb_partition
1323           do i=1,ns
1324             dyn_ss_mask(iss(i))=.true.
1325           enddo
1326       endif
1327       if (i2ndstr.gt.0) call secstrp2dihc
1328 !      call geom_to_var(nvar,x)
1329 !      call etotal(energia(0))
1330 !      call enerprint(energia(0))
1331 !      call briefout(0,etot)
1332 !      stop
1333 !d    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1334 !d    write (iout,'(a)') 'Variable list:'
1335 !d    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1336 #ifdef MPI
1337       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file)) &
1338         write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)') &
1339         'Processor',myrank,': end reading molecular data.'
1340 #endif
1341       return
1342       end subroutine molread
1343 !-----------------------------------------------------------------------------
1344 !-----------------------------------------------------------------------------
1345       end module io