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