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       c(:,:)=0.0D0
 708       dc(:,:)=0.0D0
 709       itype(:)=0
 710 !-----------------------------
 711 !
 712 ! Body
 713 !
 714 ! Read weights of the subsequent energy terms.
 715       call card_concat(weightcard,.true.)
 716       call reada(weightcard,'WLONG',wlong,1.0D0)
 717       call reada(weightcard,'WSC',wsc,wlong)
 718       call reada(weightcard,'WSCP',wscp,wlong)
 719       call reada(weightcard,'WELEC',welec,1.0D0)
 720       call reada(weightcard,'WVDWPP',wvdwpp,welec)
 721       call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 722       call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 723       call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 724       call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 725       call reada(weightcard,'WTURN3',wturn3,1.0D0)
 726       call reada(weightcard,'WTURN4',wturn4,1.0D0)
 727       call reada(weightcard,'WTURN6',wturn6,1.0D0)
 728       call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 729       call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 730       call reada(weightcard,'WBOND',wbond,1.0D0)
 731       call reada(weightcard,'WTOR',wtor,1.0D0)
 732       call reada(weightcard,'WTORD',wtor_d,1.0D0)
 733       call reada(weightcard,'WSHIELD',wshield,0.05D0)
 734       call reada(weightcard,'LIPSCALE',lipscale,1.0D0)
 735       call reada(weightcard,'WLT',wliptran,1.0D0)
 736       call reada(weightcard,'WANG',wang,1.0D0)
 737       call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 738       call reada(weightcard,'SCAL14',scal14,0.4D0)
 739       call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 740       call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 741       call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 742       call reada(weightcard,'TEMP0',temp0,300.0d0)
 743       if (index(weightcard,'SOFT').gt.0) ipot=6
 744 ! 12/1/95 Added weight for the multi-body term WCORR
 745       call reada(weightcard,'WCORRH',wcorr,1.0D0)
 746       if (wcorr4.gt.0.0d0) wcorr=wcorr4
 747       weights(1)=wsc
 748       weights(2)=wscp
 749       weights(3)=welec
 750       weights(4)=wcorr
 751       weights(5)=wcorr5
 752       weights(6)=wcorr6
 753       weights(7)=wel_loc
 754       weights(8)=wturn3
 755       weights(9)=wturn4
 756       weights(10)=wturn6
 757       weights(11)=wang
 758       weights(12)=wscloc
 759       weights(13)=wtor
 760       weights(14)=wtor_d
 761       weights(15)=wstrain
 762       weights(16)=wvdwpp
 763       weights(17)=wbond
 764       weights(18)=scal14
 765       weights(21)=wsccor
 766       if(me.eq.king.or..not.out1file) &
 767        write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
 768         wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
 769         wturn4,wturn6
 770    10 format (/'Energy-term weights (unscaled):'// &
 771        'WSCC=   ',f10.6,' (SC-SC)'/ &
 772        'WSCP=   ',f10.6,' (SC-p)'/ &
 773        'WELEC=  ',f10.6,' (p-p electr)'/ &
 774        'WVDWPP= ',f10.6,' (p-p VDW)'/ &
 775        'WBOND=  ',f10.6,' (stretching)'/ &
 776        'WANG=   ',f10.6,' (bending)'/ &
 777        'WSCLOC= ',f10.6,' (SC local)'/ &
 778        'WTOR=   ',f10.6,' (torsional)'/ &
 779        'WTORD=  ',f10.6,' (double torsional)'/ &
 780        'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
 781        'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
 782        'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
 783        'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
 784        'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
 785        'WSCCOR= ',f10.6,' (back-scloc correlation)'/ &
 786        'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
 787        'WTURN4= ',f10.6,' (turns, 4th order)'/ &
 788        'WTURN6= ',f10.6,' (turns, 6th order)')
 789       if(me.eq.king.or..not.out1file)then
 790        if (wcorr4.gt.0.0d0) then
 791         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',&
 792          'between contact pairs of peptide groups'
 793         write (iout,'(2(a,f5.3/))') &
 794         'Cutoff on 4-6th order correlation terms: ',cutoff_corr,&
 795         'Range of quenching the correlation terms:',2*delt_corr
 796        else if (wcorr.gt.0.0d0) then
 797         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',&
 798          'between contact pairs of peptide groups'
 799        endif
 800        write (iout,'(a,f8.3)') &
 801         'Scaling factor of 1,4 SC-p interactions:',scal14
 802        write (iout,'(a,f8.3)') &
 803         'General scaling factor of SC-p interactions:',scalscp
 804       endif
 805       r0_corr=cutoff_corr-delt_corr
 806       do i=1,ntyp
 807         aad(i,1)=scalscp*aad(i,1)
 808         aad(i,2)=scalscp*aad(i,2)
 809         bad(i,1)=scalscp*bad(i,1)
 810         bad(i,2)=scalscp*bad(i,2)
 811       enddo
 812       call rescale_weights(t_bath)
 813       if(me.eq.king.or..not.out1file) &
 814        write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
 815         wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
 816         wturn4,wturn6
 817    22 format (/'Energy-term weights (scaled):'// &
 818        'WSCC=   ',f10.6,' (SC-SC)'/ &
 819        'WSCP=   ',f10.6,' (SC-p)'/ &
 820        'WELEC=  ',f10.6,' (p-p electr)'/ &
 821        'WVDWPP= ',f10.6,' (p-p VDW)'/ &
 822        'WBOND=  ',f10.6,' (stretching)'/ &
 823        'WANG=   ',f10.6,' (bending)'/ &
 824        'WSCLOC= ',f10.6,' (SC local)'/ &
 825        'WTOR=   ',f10.6,' (torsional)'/ &
 826        'WTORD=  ',f10.6,' (double torsional)'/ &
 827        'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
 828        'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
 829        'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
 830        'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
 831        'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
 832        'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/ &
 833        'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
 834        'WTURN4= ',f10.6,' (turns, 4th order)'/ &
 835        'WTURN6= ',f10.6,' (turns, 6th order)')
 836       if(me.eq.king.or..not.out1file) &
 837        write (iout,*) "Reference temperature for weights calculation:",&
 838         temp0
 839       call reada(weightcard,"D0CM",d0cm,3.78d0)
 840       call reada(weightcard,"AKCM",akcm,15.1d0)
 841       call reada(weightcard,"AKTH",akth,11.0d0)
 842       call reada(weightcard,"AKCT",akct,12.0d0)
 843       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 844       call reada(weightcard,"V2SS",v2ss,7.61d0)
 845       call reada(weightcard,"V3SS",v3ss,13.7d0)
 846       call reada(weightcard,"EBR",ebr,-5.50D0)
 847       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 848
 849       call reada(weightcard,"HT",Ht,0.0D0)
 850       if (dyn_ss) then
 851         ss_depth=ebr/wsc-0.25*eps(1,1)
 852         Ht=Ht/wsc-0.25*eps(1,1)
 853         akcm=akcm*wstrain/wsc
 854         akth=akth*wstrain/wsc
 855         akct=akct*wstrain/wsc
 856         v1ss=v1ss*wstrain/wsc
 857         v2ss=v2ss*wstrain/wsc
 858         v3ss=v3ss*wstrain/wsc
 859       else
 860         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 861       endif
 862
 863       if(me.eq.king.or..not.out1file) then
 864        write (iout,*) "Parameters of the SS-bond potential:"
 865        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,&
 866        " AKCT",akct
 867        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 868        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 869        write (iout,*)" HT",Ht
 870        print *,'indpdb=',indpdb,' pdbref=',pdbref
 871       endif
 872       if (indpdb.gt.0 .or. pdbref) then
 873         read(inp,'(a)') pdbfile
 874         if(me.eq.king.or..not.out1file) &
 875          write (iout,'(2a)') 'PDB data will be read from file ',&
 876          pdbfile(:ilen(pdbfile))
 877         open(ipdbin,file=pdbfile,status='old',err=33)
 878         goto 34
 879   33    write (iout,'(a)') 'Error opening PDB file.'
 880         stop
 881   34    continue
 882 !        print *,'Begin reading pdb data'
 883         call readpdb
 884 !        print *,'Finished reading pdb data'
 885         if(me.eq.king.or..not.out1file) &
 886          write (iout,'(a,i3,a,i3)')'nsup=',nsup,&
 887          ' nstart_sup=',nstart_sup !,"ergwergewrgae"
 888 !el        if(.not.allocated(itype_pdb))
 889         allocate(itype_pdb(nres))
 890         do i=1,nres
 891           itype_pdb(i)=itype(i)
 892         enddo
 893         close (ipdbin)
 894         nnt=nstart_sup
 895         nct=nstart_sup+nsup-1
 896 !el        if(.not.allocated(icont_ref))
 897         allocate(icont_ref(2,12*nres)) ! maxcont=12*maxres
 898         call contact(.false.,ncont_ref,icont_ref,co)
 899
 900         if (sideadd) then
 901          if(me.eq.king.or..not.out1file) &
 902           write(iout,*)'Adding sidechains'
 903          maxsi=1000
 904          do i=2,nres-1
 905           iti=itype(i)
 906           if (iti.ne.10 .and. itype(i).ne.ntyp1) then
 907             nsi=0
 908             fail=.true.
 909             do while (fail.and.nsi.le.maxsi)
 910               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
 911               nsi=nsi+1
 912             enddo
 913             if(fail) write(iout,*)'Adding sidechain failed for res ',&
 914                     i,' after ',nsi,' trials'
 915           endif
 916          enddo
 917         endif
 918       endif
 919
 920       if (indpdb.eq.0) then
 921 ! Read sequence if not taken from the pdb file.
 922         read (inp,*) nres
 923 !        print *,'nres=',nres
 924         allocate(sequence(nres))
 925         if (iscode.gt.0) then
 926           read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
 927         else
 928           read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
 929         endif
 930 ! Convert sequence to numeric code
 931         do i=1,nres
 932           itype(i)=rescode(i,sequence(i),iscode)
 933         enddo
 934 ! Assign initial virtual bond lengths
 935 !elwrite(iout,*) "test_alloc"
 936         if(.not.allocated(vbld)) allocate(vbld(2*nres))
 937 !elwrite(iout,*) "test_alloc"
 938         if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
 939 !elwrite(iout,*) "test_alloc"
 940         do i=2,nres
 941           vbld(i)=vbl
 942           vbld_inv(i)=vblinv
 943         enddo
 944         do i=2,nres-1
 945           vbld(i+nres)=dsc(iabs(itype(i)))
 946           vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
 947 !          write (iout,*) "i",i," itype",itype(i),
 948 !     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
 949         enddo
 950       endif
 951 !      print *,nres
 952 !      print '(20i4)',(itype(i),i=1,nres)
 953 !----------------------------
 954 !el reallocate tables
 955 !      do i=1,maxres2
 956 !        do j=1,3
 957 !          c_alloc(j,i)=c(j,i)
 958 !          dc_alloc(j,i)=dc(j,i)
 959 !        enddo
 960 !      enddo
 961 !      do i=1,maxres
 962 !elwrite(iout,*) "itype",i,itype(i)
 963 !        itype_alloc(i)=itype(i)
 964 !      enddo
 965
 966 !      deallocate(c)
 967 !      deallocate(dc)
 968 !      deallocate(itype)
 969 !      allocate(c(3,2*nres+4))
 970 !      allocate(dc(3,0:2*nres+2))
 971 !      allocate(itype(nres+2))
 972       allocate(itel(nres+2))
 973       itel(:)=0
 974
 975 !      do i=1,2*nres+2
 976 !        do j=1,3
 977 !          c(j,i)=c_alloc(j,i)
 978 !          dc(j,i)=dc_alloc(j,i)
 979 !        enddo
 980 !      enddo
 981 !      do i=1,nres+2
 982 !        itype(i)=itype_alloc(i)
 983 !        itel(i)=0
 984 !      enddo
 985 !--------------------------
 986       do i=1,nres
 987 #ifdef PROCOR
 988         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
 989 #else
 990         if (itype(i).eq.ntyp1) then
 991 #endif
 992           itel(i)=0
 993 #ifdef PROCOR
 994         else if (iabs(itype(i+1)).ne.20) then
 995 #else
 996         else if (iabs(itype(i)).ne.20) then
 997 #endif
 998           itel(i)=1
 999         else
1000           itel(i)=2
1001         endif
1002       enddo
1003       if(me.eq.king.or..not.out1file)then
1004        write (iout,*) "ITEL"
1005        do i=1,nres-1
1006          write (iout,*) i,itype(i),itel(i)
1007        enddo
1008        print *,'Call Read_Bridge.'
1009       endif
1010       call read_bridge
1011 !--------------------------------
1012 ! znamy nres oraz nss można zaalokowac potrzebne tablice
1013       call alloc_geo_arrays
1014       call alloc_ener_arrays
1015 !--------------------------------
1016 ! 8/13/98 Set limits to generating the dihedral angles
1017       do i=1,nres
1018         phibound(1,i)=-pi
1019         phibound(2,i)=pi
1020       enddo
1021       read (inp,*) ndih_constr
1022       if (ndih_constr.gt.0) then
1023         allocate(idih_constr(ndih_constr),idih_nconstr(ndih_constr)) !(maxdih_constr)
1024         allocate(phi0(ndih_constr),drange(ndih_constr)) !(maxdih_constr)
1025         read (inp,*) ftors
1026         read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
1027         if(me.eq.king.or..not.out1file)then
1028          write (iout,*) &
1029          'There are',ndih_constr,' constraints on phi angles.'
1030          do i=1,ndih_constr
1031           write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
1032          enddo
1033         endif
1034         do i=1,ndih_constr
1035           phi0(i)=deg2rad*phi0(i)
1036           drange(i)=deg2rad*drange(i)
1037         enddo
1038         if(me.eq.king.or..not.out1file) &
1039          write (iout,*) 'FTORS',ftors
1040         do i=1,ndih_constr
1041           ii = idih_constr(i)
1042           phibound(1,ii) = phi0(i)-drange(i)
1043           phibound(2,ii) = phi0(i)+drange(i)
1044         enddo
1045       endif
1046       nnt=1
1047 #ifdef MPI
1048       if (me.eq.king) then
1049 #endif
1050        write (iout,'(a)') 'Boundaries in phi angle sampling:'
1051        do i=1,nres
1052          write (iout,'(a3,i5,2f10.1)') &
1053          restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1054        enddo
1055 #ifdef MP
1056       endif
1057 #endif
1058       nct=nres
1059 !d      print *,'NNT=',NNT,' NCT=',NCT
1060       if (itype(1).eq.ntyp1) nnt=2
1061       if (itype(nres).eq.ntyp1) nct=nct-1
1062       if (pdbref) then
1063         if(me.eq.king.or..not.out1file) &
1064          write (iout,'(a,i3)') 'nsup=',nsup
1065         nstart_seq=nnt
1066         if (nsup.le.(nct-nnt+1)) then
1067           do i=0,nct-nnt+1-nsup
1068             if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
1069               nstart_seq=nnt+i
1070               goto 111
1071             endif
1072           enddo
1073           write (iout,'(a)') &
1074                   'Error - sequences to be superposed do not match.'
1075           stop
1076         else
1077           do i=0,nsup-(nct-nnt+1)
1078             if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1)) &
1079             then
1080               nstart_sup=nstart_sup+i
1081               nsup=nct-nnt+1
1082               goto 111
1083             endif
1084           enddo
1085           write (iout,'(a)') &
1086                   'Error - sequences to be superposed do not match.'
1087         endif
1088   111   continue
1089         if (nsup.eq.0) nsup=nct-nnt
1090         if (nstart_sup.eq.0) nstart_sup=nnt
1091         if (nstart_seq.eq.0) nstart_seq=nnt
1092         if(me.eq.king.or..not.out1file) &
1093          write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,&
1094                        ' nstart_seq=',nstart_seq !,"242343453254"
1095       endif
1096 !--- Zscore rms -------
1097       if (nz_start.eq.0) nz_start=nnt
1098       if (nz_end.eq.0 .and. nsup.gt.0) then
1099         nz_end=nnt+nsup-1
1100       else if (nz_end.eq.0) then
1101         nz_end=nct
1102       endif
1103       if(me.eq.king.or..not.out1file)then
1104        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1105        write (iout,*) 'IZ_SC=',iz_sc
1106       endif
1107 !----------------------
1108       call init_int_table
1109       if (refstr) then
1110         if (.not.pdbref) then
1111           call read_angles(inp,*38)
1112           goto 39
1113    38     write (iout,'(a)') 'Error reading reference structure.'
1114 #ifdef MPI
1115           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1116           stop 'Error reading reference structure'
1117 #endif
1118    39     call chainbuild
1119           call setup_var
1120 !zscore          call geom_to_var(nvar,coord_exp_zs(1,1))
1121           nstart_sup=nnt
1122           nstart_seq=nnt
1123           nsup=nct-nnt+1
1124           kkk=1
1125           do i=1,2*nres
1126             do j=1,3
1127               cref(j,i,kkk)=c(j,i)
1128             enddo
1129           enddo
1130           call contact(.true.,ncont_ref,icont_ref,co)
1131         endif
1132 !        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1133         call flush(iout)
1134         if (constr_dist.gt.0) call read_dist_constr
1135         write (iout,*) "After read_dist_constr nhpb",nhpb
1136         call hpb_partition
1137         if(me.eq.king.or..not.out1file) &
1138          write (iout,*) 'Contact order:',co
1139         if (pdbref) then
1140         if(me.eq.king.or..not.out1file) &
1141          write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1142         do i=1,ncont_ref
1143           do j=1,2
1144             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1145           enddo
1146           if(me.eq.king.or..not.out1file) &
1147            write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',&
1148            icont_ref(1,i),' ',&
1149            restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
1150         enddo
1151         endif
1152       endif
1153       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 &
1154           .and. modecalc.ne.8 .and. modecalc.ne.9 .and. &
1155           modecalc.ne.10) then
1156 ! If input structure hasn't been supplied from the PDB file read or generate
1157 ! initial geometry.
1158         if (iranconf.eq.0 .and. .not. extconf) then
1159           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) &
1160            write (iout,'(a)') 'Initial geometry will be read in.'
1161           if (read_cart) then
1162             read(inp,'(8f10.5)',end=36,err=36) &
1163              ((c(l,k),l=1,3),k=1,nres),&
1164              ((c(l,k+nres),l=1,3),k=nnt,nct)
1165             write (iout,*) "Exit READ_CART"
1166             write (iout,'(8f10.5)') &
1167              ((c(l,k),l=1,3),k=1,nres),&
1168              ((c(l,k+nres),l=1,3),k=nnt,nct)
1169             call int_from_cart1(.true.)
1170             write (iout,*) "Finish INT_TO_CART"
1171             do i=1,nres-1
1172               do j=1,3
1173                 dc(j,i)=c(j,i+1)-c(j,i)
1174                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1175               enddo
1176             enddo
1177             do i=nnt,nct
1178               if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
1179                 do j=1,3
1180                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
1181                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1182                 enddo
1183               endif
1184             enddo
1185             return
1186           else
1187             call read_angles(inp,*36)
1188           endif
1189           goto 37
1190    36     write (iout,'(a)') 'Error reading angle file.'
1191 #ifdef MPI
1192           call mpi_finalize( MPI_COMM_WORLD,IERR )
1193 #endif
1194           stop 'Error reading angle file.'
1195    37     continue
1196         else if (extconf) then
1197          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0) &
1198           write (iout,'(a)') 'Extended chain initial geometry.'
1199          do i=3,nres
1200           theta(i)=90d0*deg2rad
1201          enddo
1202          do i=4,nres
1203           phi(i)=180d0*deg2rad
1204          enddo
1205          do i=2,nres-1
1206           alph(i)=110d0*deg2rad
1207          enddo
1208 !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
1209          do i=2,nres-1
1210           omeg(i)=-120d0*deg2rad
1211           if (itype(i).le.0) omeg(i)=-omeg(i)
1212          enddo
1213         else
1214           if(me.eq.king.or..not.out1file) &
1215            write (iout,'(a)') 'Random-generated initial geometry.'
1216
1217
1218 #ifdef MPI
1219           if (me.eq.king  .or. fg_rank.eq.0 .and. &
1220                  ( modecalc.eq.12 .or. modecalc.eq.14) ) then
1221 #endif
1222             do itrial=1,100
1223               itmp=1
1224               call gen_rand_conf(itmp,*30)
1225               goto 40
1226    30         write (iout,*) 'Failed to generate random conformation',&
1227                 ', itrial=',itrial
1228               write (*,*) 'Processor:',me,&
1229                 ' Failed to generate random conformation',&
1230                 ' itrial=',itrial
1231               call intout
1232
1233 #ifdef AIX
1234               call flush_(iout)
1235 #else
1236               call flush(iout)
1237 #endif
1238             enddo
1239             write (iout,'(a,i3,a)') 'Processor:',me,&
1240               ' error in generating random conformation.'
1241             write (*,'(a,i3,a)') 'Processor:',me,&
1242               ' error in generating random conformation.'
1243             call flush(iout)
1244 #ifdef MPI
1245             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1246    40       continue
1247           endif
1248 #else
1249           do itrial=1,100
1250             itmp=1
1251             call gen_rand_conf(itmp,*335)
1252             goto 40
1253   335       write (iout,*) 'Failed to generate random conformation',&
1254               ', itrial=',itrial
1255             write (*,*) 'Failed to generate random conformation',&
1256               ', itrial=',itrial
1257           enddo
1258           write (iout,'(a,i3,a)') 'Processor:',me,&
1259             ' error in generating random conformation.'
1260           write (*,'(a,i3,a)') 'Processor:',me,&
1261             ' error in generating random conformation.'
1262           stop
1263    40     continue
1264 #endif
1265         endif
1266       elseif (modecalc.eq.4) then
1267         read (inp,'(a)') intinname
1268         open (intin,file=intinname,status='old',err=333)
1269         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0) &
1270         write (iout,'(a)') 'intinname',intinname
1271         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1272         goto 334
1273   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1274 #ifdef MPI
1275         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1276 #endif
1277         stop 'Error opening angle file.'
1278   334   continue
1279
1280       endif
1281 ! Generate distance constraints, if the PDB structure is to be regularized.
1282       if (nthread.gt.0) then
1283         call read_threadbase
1284       endif
1285       call setup_var
1286 !elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
1287       if (me.eq.king .or. .not. out1file) &
1288        call intout
1289 !elwrite (iout,*)"alph(i)*rad2deg",(alph(i)*rad2deg, i=1,nres)
1290       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1291         write (iout,'(/a,i3,a)') &
1292         'The chain contains',ns,' disulfide-bridging cysteines.'
1293         write (iout,'(20i4)') (iss(i),i=1,ns)
1294        if (dyn_ss) then
1295           write(iout,*)"Running with dynamic disulfide-bond formation"
1296        else
1297         write (iout,'(/a/)') 'Pre-formed links are:'
1298         do i=1,nss
1299           i1=ihpb(i)-nres
1300           i2=jhpb(i)-nres
1301           it1=itype(i1)
1302           it2=itype(i2)
1303           if (me.eq.king.or..not.out1file) &
1304           write (iout,'(2a,i3,3a,i3,a,3f10.3)') &
1305           restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),&
1306           ebr,forcon(i)
1307         enddo
1308         write (iout,'(a)')
1309        endif
1310       endif
1311       if (ns.gt.0.and.dyn_ss) then
1312           do i=nss+1,nhpb
1313             ihpb(i-nss)=ihpb(i)
1314             jhpb(i-nss)=jhpb(i)
1315             forcon(i-nss)=forcon(i)
1316             dhpb(i-nss)=dhpb(i)
1317           enddo
1318           nhpb=nhpb-nss
1319           nss=0
1320           call hpb_partition
1321           do i=1,ns
1322             dyn_ss_mask(iss(i))=.true.
1323           enddo
1324       endif
1325       if (i2ndstr.gt.0) call secstrp2dihc
1326 !      call geom_to_var(nvar,x)
1327 !      call etotal(energia(0))
1328 !      call enerprint(energia(0))
1329 !      call briefout(0,etot)
1330 !      stop
1331 !d    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1332 !d    write (iout,'(a)') 'Variable list:'
1333 !d    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1334 #ifdef MPI
1335       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file)) &
1336         write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)') &
1337         'Processor',myrank,': end reading molecular data.'
1338 #endif
1339       return
1340       end subroutine molread
1341 !-----------------------------------------------------------------------------
1342 !-----------------------------------------------------------------------------
1343       end module io