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,1).ne.10) then
 224 !d             print *,'i=',i,' itype=',itype(i,1),' theta=',theta(i+1)
 225                fail=.true.
 226                ii=0
 227                do while (fail .and. ii .le. maxsi)
 228                  call gen_side(itype(i,1),theta(i+1),alph(i),omeg(i),fail,molnum(i))
 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
 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,j
 517       real(kind=8) :: rms,frac,frac_nn,co,distance
 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 (AFMlog.gt.0) then
 531        if (refstr) then
 532          call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
 533           write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,4f12.3,i5,$)')&
 534                itime,totT,EK,potE,totE,&
 535                rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
 536                potEcomp(23),me
 537           format1="a133"
 538          else
 539 !C          print *,'A CHUJ',potEcomp(23)
 540           write (line1,'(i10,f15.2,7f12.3,i5,$)') &
 541                 itime,totT,EK,potE,totE,&
 542                 kinetic_T,t_bath,gyrate(),&
 543                 potEcomp(23),me
 544           format1="a114"
 545         endif
 546        else if (selfguide.gt.0) then
 547        distance=0.0
 548        do j=1,3
 549        distance=distance+(c(j,afmend)-c(j,afmbeg))**2
 550        enddo
 551        distance=dsqrt(distance)
 552        if (refstr) then
 553          call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
 554           write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,f12.3,f10.1,2f8.2, &
 555          f9.3,i5,$)') &
 556                itime,totT,EK,potE,totE,&
 557                rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
 558                distance,potEcomp(23),me
 559           format1="a133"
 560 !C          print *,"CHUJOWO"
 561          else
 562 !C          print *,'A CHUJ',potEcomp(23)
 563           write (line1,'(i10,f15.2,8f12.3,i5,$)')&
 564                 itime,totT,EK,potE,totE, &
 565                 kinetic_T,t_bath,gyrate(),&
 566                 distance,potEcomp(23),me
 567           format1="a114"
 568         endif
 569        else
 570        if (refstr) then
 571          call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
 572           write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)') &
 573                 itime,totT,EK,potE,totE,&
 574                 rms,frac,frac_nn,co,amax,kinetic_T,t_bath,gyrate(),me
 575           format1="a133"
 576         else
 577           write (line1,'(i10,f15.2,7f12.3,i5,$)') &
 578                  itime,totT,EK,potE,totE,&
 579                  amax,kinetic_T,t_bath,gyrate(),me
 580           format1="a114"
 581         endif
 582         ENDIF
 583         if(usampl.and.totT.gt.eq_time) then
 584            write(line2,'(i5,2f9.4,300f7.4)') iset,uconst,uconst_back,&
 585             (qfrag(ii1),ii1=1,nfrag),(qpair(ii2),ii2=1,npair),&
 586             (utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
 587            write(format2,'(a1,i3.3)') "a",23+7*nfrag+7*npair &
 588                    +21*nfrag_back
 589         else
 590            format2="a001"
 591            line2=' '
 592         endif
 593         if (print_compon) then
 594           if(itime.eq.0) then
 595            write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,&
 596                                                            ",20a12)"
 597            write (istat,format) "#","",&
 598             (ename(print_order(i)),i=1,nprint_ene)
 599           endif
 600           write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,&
 601                                                            ",20f12.3)"
 602           write (istat,format) line1,line2,&
 603             (potEcomp(print_order(i)),i=1,nprint_ene)
 604         else
 605           write(format,'(a1,a4,a1,a4,a1)') "(",format1,",",format2,")"
 606           write (istat,format) line1,line2
 607         endif
 608 #if defined(AIX)
 609         call flush(istat)
 610 #else
 611         close(istat)
 612 #endif
 613       return
 614       end subroutine  statout
 615 !-----------------------------------------------------------------------------
 616 ! readrtns_CSA.F
 617 !-----------------------------------------------------------------------------
 618       subroutine readrtns
 619
 620       use control_data
 621       use energy_data
 622       use MPI_data
 623       use muca_md, only:read_muca
 624 !      implicit real*8 (a-h,o-z)
 625 !      include 'DIMENSIONS'
 626 #ifdef MPI
 627       include 'mpif.h'
 628 #endif
 629 !      include 'COMMON.SETUP'
 630 !      include 'COMMON.CONTROL'
 631 !      include 'COMMON.SBRIDGE'
 632 !      include 'COMMON.IOUNITS'
 633       logical :: file_exist
 634       integer :: i
 635 ! Read force-field parameters except weights
 636 !      call parmread
 637 ! Read job setup parameters
 638       call read_control
 639 ! Read force-field parameters except weights
 640       call parmread
 641
 642 ! Read control parameters for energy minimzation if required
 643       if (minim) call read_minim
 644 ! Read MCM control parameters if required
 645       if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
 646 ! Read MD control parameters if reqjuired
 647       if (modecalc.eq.12) call read_MDpar
 648 ! Read MREMD control parameters if required
 649       if (modecalc.eq.14) then
 650          call read_MDpar
 651          call read_REMDpar
 652       endif
 653 ! Read MUCA control parameters if required
 654       if (lmuca) call read_muca
 655 ! Read CSA control parameters if required (from fort.40 if exists
 656 ! otherwise from general input file)
 657       if (modecalc.eq.8) then
 658        inquire (file="fort.40",exist=file_exist)
 659        if (.not.file_exist) call csaread
 660       endif
 661 !fmc      if (modecalc.eq.10) call mcmfread
 662 ! Read molecule information, molecule geometry, energy-term weights, and
 663 ! restraints if requested
 664       call molread
 665 ! Print restraint information
 666 #ifdef MPI
 667       if (.not. out1file .or. me.eq.king) then
 668 #endif
 669       if (nhpb.gt.nss) &
 670       write (iout,'(a,i5,a)') "The following",nhpb-nss,&
 671        " distance constraints have been imposed"
 672       do i=nss+1,nhpb
 673         write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
 674       enddo
 675 #ifdef MPI
 676       endif
 677 #endif
 678 !      print *,"Processor",myrank," leaves READRTNS"
 679 !      write(iout,*) "end readrtns"
 680       return
 681       end subroutine readrtns
 682 !-----------------------------------------------------------------------------
 683       subroutine molread
 684 !
 685 ! Read molecular data.
 686 !
 687 !      use control, only: ilen
 688       use control_data
 689       use geometry_data
 690       use energy_data
 691       use energy
 692       use compare_data
 693       use MD_data, only: t_bath
 694       use MPI_data
 695       use compare, only:seq_comp,contact
 696       use control
 697 !      implicit real*8 (a-h,o-z)
 698 !      include 'DIMENSIONS'
 699 #ifdef MPI
 700       include 'mpif.h'
 701       integer :: error_msg,ierror,ierr,ierrcode
 702 #endif
 703 !      include 'COMMON.IOUNITS'
 704 !      include 'COMMON.GEO'
 705 !      include 'COMMON.VAR'
 706 !      include 'COMMON.INTERACT'
 707 !      include 'COMMON.LOCAL'
 708 !      include 'COMMON.NAMES'
 709 !      include 'COMMON.CHAIN'
 710 !      include 'COMMON.FFIELD'
 711 !      include 'COMMON.SBRIDGE'
 712 !      include 'COMMON.HEADER'
 713 !      include 'COMMON.CONTROL'
 714 !      include 'COMMON.DBASE'
 715 !      include 'COMMON.THREAD'
 716 !      include 'COMMON.CONTACTS'
 717 !      include 'COMMON.TORCNSTR'
 718 !      include 'COMMON.TIME1'
 719 !      include 'COMMON.BOUNDS'
 720 !      include 'COMMON.MD'
 721 !      include 'COMMON.SETUP'
 722       character(len=4),dimension(:,:),allocatable :: sequence   !(maxres,maxmolecules)
 723 !      integer :: rescode
 724 !      double precision x(maxvar)
 725       character(len=256) :: pdbfile
 726       character(len=800) :: weightcard
 727       character(len=80) :: weightcard_t!,ucase
 728 !      integer,dimension(:),allocatable :: itype_pdb    !(maxres)
 729 !      common /pizda/ itype_pdb
 730       logical :: fail   !seq_comp,
 731       real(kind=8) :: energia(0:n_ene)
 732 !      integer ilen
 733 !el      external ilen
 734 !el local varables
 735       integer :: i,j,l,k,kkk,ii,i1,i2,it1,it2
 736
 737       real(kind=8),dimension(3,maxres2+2) :: c_alloc
 738       real(kind=8),dimension(3,0:maxres2) :: dc_alloc
 739       real(kind=8),dimension(:,:), allocatable :: secprob
 740       integer,dimension(maxres) :: itype_alloc
 741
 742       integer :: iti,nsi,maxsi,itrial,itmp
 743       real(kind=8) :: wlong,scalscp,co,ssscale,phihel,phibet,sigmahel,&
 744       sigmabet,sumv
 745       allocate(weights(n_ene))
 746 !-----------------------------
 747       allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres
 748       allocate(dc(3,0:2*maxres)) !(3,0:maxres2)
 749       allocate(itype(maxres,5)) !(maxres)
 750       allocate(istype(maxres))
 751 !
 752 ! Zero out tables.
 753 !
 754       c(:,:)=0.0D0
 755       dc(:,:)=0.0D0
 756       itype(:,:)=0
 757 !-----------------------------
 758 !
 759 ! Body
 760 !
 761 ! Read weights of the subsequent energy terms.
 762       call card_concat(weightcard,.true.)
 763       call reada(weightcard,'WLONG',wlong,1.0D0)
 764       call reada(weightcard,'WSC',wsc,wlong)
 765       call reada(weightcard,'WSCP',wscp,wlong)
 766       call reada(weightcard,'WELEC',welec,1.0D0)
 767       call reada(weightcard,'WVDWPP',wvdwpp,welec)
 768       call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 769       call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 770       call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 771       call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 772       call reada(weightcard,'WTURN3',wturn3,1.0D0)
 773       call reada(weightcard,'WTURN4',wturn4,1.0D0)
 774       call reada(weightcard,'WTURN6',wturn6,1.0D0)
 775       call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 776       call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 777       call reada(weightcard,'WVDWPP_NUCL',wvdwpp_nucl,0.0D0)
 778       call reada(weightcard,'WELPP',welpp,0.0d0)
 779       call reada(weightcard,'WVDWPSB',wvdwpsb,0.0d0)
 780       call reada(weightcard,'WELPSB',welpsb,0.0D0)
 781       call reada(weightcard,'WVDWSB',wvdwsb,0.0d0)
 782       call reada(weightcard,'WELSB',welsb,0.0D0)
 783       call reada(weightcard,'WBOND_NUCL',wbond_nucl,0.0D0)
 784       call reada(weightcard,'WANG_NUCL',wang_nucl,0.0D0)
 785       call reada(weightcard,'WSBLOC',wsbloc,0.0D0)
 786       call reada(weightcard,'WTOR_NUCL',wtor_nucl,0.0D0)
 787 !      print *,"KUR..",wtor_nucl
 788       call reada(weightcard,'WTORD_NUCL',wtor_d_nucl,0.0D0)
 789       call reada(weightcard,'WCORR_NUCL',wcorr_nucl,0.0D0)
 790       call reada(weightcard,'WCORR3_NUC',wcorr3_nucl,0.0D0)
 791       call reada(weightcard,'WBOND',wbond,1.0D0)
 792       call reada(weightcard,'WTOR',wtor,1.0D0)
 793       call reada(weightcard,'WTORD',wtor_d,1.0D0)
 794       call reada(weightcard,'WSHIELD',wshield,0.05D0)
 795       call reada(weightcard,'LIPSCALE',lipscale,1.0D0)
 796       call reada(weightcard,'WLT',wliptran,1.0D0)
 797       call reada(weightcard,'WTUBE',wtube,1.0d0)
 798       call reada(weightcard,'WANG',wang,1.0D0)
 799       call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 800       call reada(weightcard,'SCAL14',scal14,0.4D0)
 801       call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 802       call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 803       call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 804       call reada(weightcard,'TEMP0',temp0,300.0d0)
 805       call reada(weightcard,'WSCBASE',wscbase,0.0D0)
 806       if (index(weightcard,'SOFT').gt.0) ipot=6
 807       call reada(weightcard,'WBOND_NUCL',wbond_nucl,0.0D0)
 808       call reada(weightcard,'WCATCAT',wcatcat,0.0d0)
 809       call reada(weightcard,'WCATPROT',wcatprot,0.0d0)
 810       call reada(weightcard,'WCATNUCL',wcatnucl,0.0d0)
 811       call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
 812       call reada(weightcard,'WSCPHO',wscpho,0.0d0)
 813       call reada(weightcard,'WPEPPHO',wpeppho,0.0d0)
 814
 815 ! 12/1/95 Added weight for the multi-body term WCORR
 816       call reada(weightcard,'WCORRH',wcorr,1.0D0)
 817       if (wcorr4.gt.0.0d0) wcorr=wcorr4
 818       weights(1)=wsc
 819       weights(2)=wscp
 820       weights(3)=welec
 821       weights(4)=wcorr
 822       weights(5)=wcorr5
 823       weights(6)=wcorr6
 824       weights(7)=wel_loc
 825       weights(8)=wturn3
 826       weights(9)=wturn4
 827       weights(10)=wturn6
 828       weights(11)=wang
 829       weights(12)=wscloc
 830       weights(13)=wtor
 831       weights(14)=wtor_d
 832       weights(15)=wstrain
 833       weights(16)=wvdwpp
 834       weights(17)=wbond
 835       weights(18)=scal14
 836       weights(21)=wsccor
 837           weights(26)=wvdwpp_nucl
 838           weights(27)=welpp
 839           weights(28)=wvdwpsb
 840           weights(29)=welpsb
 841           weights(30)=wvdwsb
 842           weights(31)=welsb
 843           weights(32)=wbond_nucl
 844           weights(33)=wang_nucl
 845           weights(34)=wsbloc
 846           weights(35)=wtor_nucl
 847           weights(36)=wtor_d_nucl
 848           weights(37)=wcorr_nucl
 849           weights(38)=wcorr3_nucl
 850           weights(41)=wcatcat
 851           weights(42)=wcatprot
 852           weights(46)=wscbase
 853           weights(47)=wpepbase
 854           weights(48)=wscpho
 855           weights(49)=wpeppho
 856           weights(50)=wcatnucl
 857
 858       if(me.eq.king.or..not.out1file) &
 859        write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
 860         wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
 861         wturn4,wturn6
 862    10 format (/'Energy-term weights (unscaled):'// &
 863        'WSCC=   ',f10.6,' (SC-SC)'/ &
 864        'WSCP=   ',f10.6,' (SC-p)'/ &
 865        'WELEC=  ',f10.6,' (p-p electr)'/ &
 866        'WVDWPP= ',f10.6,' (p-p VDW)'/ &
 867        'WBOND=  ',f10.6,' (stretching)'/ &
 868        'WANG=   ',f10.6,' (bending)'/ &
 869        'WSCLOC= ',f10.6,' (SC local)'/ &
 870        'WTOR=   ',f10.6,' (torsional)'/ &
 871        'WTORD=  ',f10.6,' (double torsional)'/ &
 872        'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
 873        'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
 874        'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
 875        'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
 876        'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
 877        'WSCCOR= ',f10.6,' (back-scloc correlation)'/ &
 878        'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
 879        'WTURN4= ',f10.6,' (turns, 4th order)'/ &
 880        'WTURN6= ',f10.6,' (turns, 6th order)')
 881       if(me.eq.king.or..not.out1file)then
 882        if (wcorr4.gt.0.0d0) then
 883         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',&
 884          'between contact pairs of peptide groups'
 885         write (iout,'(2(a,f5.3/))') &
 886         'Cutoff on 4-6th order correlation terms: ',cutoff_corr,&
 887         'Range of quenching the correlation terms:',2*delt_corr
 888        else if (wcorr.gt.0.0d0) then
 889         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',&
 890          'between contact pairs of peptide groups'
 891        endif
 892        write (iout,'(a,f8.3)') &
 893         'Scaling factor of 1,4 SC-p interactions:',scal14
 894        write (iout,'(a,f8.3)') &
 895         'General scaling factor of SC-p interactions:',scalscp
 896       endif
 897       r0_corr=cutoff_corr-delt_corr
 898       do i=1,ntyp
 899         aad(i,1)=scalscp*aad(i,1)
 900         aad(i,2)=scalscp*aad(i,2)
 901         bad(i,1)=scalscp*bad(i,1)
 902         bad(i,2)=scalscp*bad(i,2)
 903       enddo
 904       call rescale_weights(t_bath)
 905       if(me.eq.king.or..not.out1file) &
 906        write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
 907         wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,&
 908         wturn4,wturn6
 909    22 format (/'Energy-term weights (scaled):'// &
 910        'WSCC=   ',f10.6,' (SC-SC)'/ &
 911        'WSCP=   ',f10.6,' (SC-p)'/ &
 912        'WELEC=  ',f10.6,' (p-p electr)'/ &
 913        'WVDWPP= ',f10.6,' (p-p VDW)'/ &
 914        'WBOND=  ',f10.6,' (stretching)'/ &
 915        'WANG=   ',f10.6,' (bending)'/ &
 916        'WSCLOC= ',f10.6,' (SC local)'/ &
 917        'WTOR=   ',f10.6,' (torsional)'/ &
 918        'WTORD=  ',f10.6,' (double torsional)'/ &
 919        'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ &
 920        'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ &
 921        'WCORR4= ',f10.6,' (multi-body 4th order)'/ &
 922        'WCORR5= ',f10.6,' (multi-body 5th order)'/ &
 923        'WCORR6= ',f10.6,' (multi-body 6th order)'/ &
 924        'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/ &
 925        'WTURN3= ',f10.6,' (turns, 3rd order)'/ &
 926        'WTURN4= ',f10.6,' (turns, 4th order)'/ &
 927        'WTURN6= ',f10.6,' (turns, 6th order)')
 928       if(me.eq.king.or..not.out1file) &
 929        write (iout,*) "Reference temperature for weights calculation:",&
 930         temp0
 931       call reada(weightcard,"D0CM",d0cm,3.78d0)
 932       call reada(weightcard,"AKCM",akcm,15.1d0)
 933       call reada(weightcard,"AKTH",akth,11.0d0)
 934       call reada(weightcard,"AKCT",akct,12.0d0)
 935       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 936       call reada(weightcard,"V2SS",v2ss,7.61d0)
 937       call reada(weightcard,"V3SS",v3ss,13.7d0)
 938       call reada(weightcard,"EBR",ebr,-5.50D0)
 939       call reada(weightcard,"ATRISS",atriss,0.301D0)
 940       call reada(weightcard,"BTRISS",btriss,0.021D0)
 941       call reada(weightcard,"CTRISS",ctriss,1.001D0)
 942       call reada(weightcard,"DTRISS",dtriss,1.001D0)
 943       call reada(weightcard,"SSSCALE",ssscale,1.0D0)
 944       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 945
 946       call reada(weightcard,"HT",Ht,0.0D0)
 947       if (dyn_ss) then
 948        ss_depth=(ebr/wsc-0.25*eps(1,1))*ssscale
 949         Ht=(Ht/wsc-0.25*eps(1,1))*ssscale
 950         akcm=akcm/wsc*ssscale
 951         akth=akth/wsc*ssscale
 952         akct=akct/wsc*ssscale
 953         v1ss=v1ss/wsc*ssscale
 954         v2ss=v2ss/wsc*ssscale
 955         v3ss=v3ss/wsc*ssscale
 956       else
 957         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 958       endif
 959
 960       if(me.eq.king.or..not.out1file) then
 961        write (iout,*) "Parameters of the SS-bond potential:"
 962        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,&
 963        " AKCT",akct
 964        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 965        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 966        write (iout,*)" HT",Ht
 967        print *,'indpdb=',indpdb,' pdbref=',pdbref
 968       endif
 969       if (indpdb.gt.0 .or. pdbref) then
 970         read(inp,'(a)') pdbfile
 971         if(me.eq.king.or..not.out1file) &
 972          write (iout,'(2a)') 'PDB data will be read from file ',&
 973          pdbfile(:ilen(pdbfile))
 974         open(ipdbin,file=pdbfile,status='old',err=33)
 975         goto 34
 976   33    write (iout,'(a)') 'Error opening PDB file.'
 977         stop
 978   34    continue
 979 !        print *,'Begin reading pdb data'
 980         call readpdb
 981 !        call int_from_cart1(.true.)
 982
 983 !        print *,'Finished reading pdb data'
 984         if(me.eq.king.or..not.out1file) &
 985          write (iout,'(a,i3,a,i3)')'nsup=',nsup,&
 986          ' nstart_sup=',nstart_sup !,"ergwergewrgae"
 987 !el        if(.not.allocated(itype_pdb))
 988         allocate(itype_pdb(nres))
 989         do i=1,nres
 990           itype_pdb(i)=itype(i,1)
 991         enddo
 992         close (ipdbin)
 993         nnt=nstart_sup
 994         nct=nstart_sup+nsup-1
 995 !el        if(.not.allocated(icont_ref))
 996         allocate(icont_ref(2,(nres/2)*nres)) ! maxcont=12*maxres
 997         call contact(.false.,ncont_ref,icont_ref,co)
 998
 999         if (sideadd) then
1000          if(me.eq.king.or..not.out1file) &
1001           write(iout,*)'Adding sidechains'
1002          maxsi=1000
1003          do i=2,nres-1
1004           iti=itype(i,1)
1005           if (iti.ne.10 .and. itype(i,1).ne.ntyp1) then
1006             nsi=0
1007             fail=.true.
1008             do while (fail.and.nsi.le.maxsi)
1009               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1010               nsi=nsi+1
1011             enddo
1012             if(fail) write(iout,*)'Adding sidechain failed for res ',&
1013                     i,' after ',nsi,' trials'
1014           endif
1015          enddo
1016         endif
1017       endif
1018       print *,"CZY TU DOCHODZE"
1019       if (indpdb.eq.0) then
1020       nres_molec(:)=0
1021         allocate(sequence(maxres,5))
1022 !      itype(:,:)=0
1023       itmp=0
1024       if (protein) then
1025 ! Read sequence if not taken from the pdb file.
1026         molec=1
1027         read (inp,*) nres_molec(molec)
1028         print *,'nres=',nres
1029         if (iscode.gt.0) then
1030           read (inp,'(80a1)') (sequence(i,molec)(1:1),i=1,nres_molec(molec))
1031         else
1032           read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
1033         endif
1034 !        read(inp,*) weightcard_t
1035 !        print *,"po seq" weightcard_t
1036 ! Convert sequence to numeric code
1037
1038         do i=1,nres_molec(molec)
1039           itmp=itmp+1
1040           itype(i,1)=rescode(i,sequence(i,molec),iscode,molec)
1041           print *,itype(i,1)
1042
1043         enddo
1044        endif
1045 !        read(inp,*) weightcard_t
1046 !        print *,"po seq", weightcard_t
1047
1048        if (nucleic) then
1049 ! Read sequence if not taken from the pdb file.
1050         molec=2
1051         read (inp,*) nres_molec(molec)
1052         print *,'nres=',nres_molec(molec)
1053 !        allocate(sequence(maxres,5))
1054 !        if (iscode.gt.0) then
1055           read (inp,'(20a4)') (sequence(i,molec),i=1,nres_molec(molec))
1056           print *,"KUR**"
1057           print *,(sequence(i,molec),i=1,nres_molec(molec))
1058 ! Convert sequence to numeric code
1059
1060         do i=1,nres_molec(molec)
1061           itmp=itmp+1
1062           istype(itmp)=sugarcode(sequence(i,molec)(1:1),i)
1063           sequence(i,molec)=sequence(i,molec)(1:2)
1064           itype(itmp,molec)=rescode(i,sequence(i,molec),iscode,molec)
1065           write(iout,*) "NUCLE=", itype(itmp,molec)
1066         enddo
1067        endif
1068
1069        if (ions) then
1070 ! Read sequence if not taken from the pdb file.
1071         molec=5
1072         read (inp,*) nres_molec(molec)
1073 !        print *,'nres=',nres
1074           read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
1075 ! Convert sequence to numeric code
1076         print *,nres_molec(molec)
1077         do i=1,nres_molec(molec)
1078           itmp=itmp+1
1079           print *,itmp,"itmp"
1080           itype(itmp,molec)=rescode(i,sequence(i,molec),iscode,molec)
1081         enddo
1082        endif
1083        nres=0
1084        do i=1,5
1085         nres=nres+nres_molec(i)
1086         print *,"nres_molec",nres,nres_molec(i)
1087        enddo
1088
1089 ! Assign initial virtual bond lengths
1090         if(.not.allocated(molnum)) then
1091          allocate(molnum(nres+1))
1092          itmp=0
1093         do i=1,5
1094                do j=1,nres_molec(i)
1095                itmp=itmp+1
1096               molnum(itmp)=i
1097                enddo
1098          enddo
1099 !        print *,nres_molec(i)
1100         endif
1101         print *,nres,"nres"
1102         if(.not.allocated(vbld)) then
1103            print *, "I DO ENTER"
1104            allocate(vbld(2*nres))
1105         endif
1106         if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
1107         do i=2,nres
1108           if (molnum(i).eq.1) then
1109           vbld(i)=vbl
1110           vbld_inv(i)=vblinv
1111
1112           else
1113           vbld(i)=7.0
1114           vbld_inv(i)=1.0/7.0
1115           endif
1116         enddo
1117         do i=2,nres-1
1118            if (molnum(i).eq.1) then
1119 !          print *, "molnum",molnum(i),itype(i,molnum(i)),nres,i
1120           vbld(i+nres)=dsc(iabs(itype(i,molnum(i))))
1121           vbld_inv(i+nres)=dsc_inv(iabs(itype(i,molnum(i))))
1122            else
1123           vbld(i+nres)=vbldsc0_nucl(1,iabs(itype(i,molnum(i))))
1124           vbld_inv(i+nres)=1.0/vbldsc0_nucl(1,iabs(itype(i,molnum(i))))
1125            endif
1126 !          write (iout,*) "i",i," itype",itype(i,1),
1127 !     &      " dsc",dsc(itype(i,1))," vbld",vbld(i),vbld(i+nres)
1128         enddo
1129       endif
1130 !      print *,nres
1131 !      print '(20i4)',(itype(i,1),i=1,nres)
1132 !----------------------------
1133 !el reallocate tables
1134 !      do i=1,maxres2
1135 !        do j=1,3
1136 !          c_alloc(j,i)=c(j,i)
1137 !          dc_alloc(j,i)=dc(j,i)
1138 !        enddo
1139 !      enddo
1140 !      do i=1,maxres
1141 !elwrite(iout,*) "itype",i,itype(i,1)
1142 !        itype_alloc(i)=itype(i,1)
1143 !      enddo
1144
1145 !      deallocate(c)
1146 !      deallocate(dc)
1147 !      deallocate(itype)
1148 !      allocate(c(3,2*nres+4))
1149 !      allocate(dc(3,0:2*nres+2))
1150 !      allocate(itype(nres+2))
1151       allocate(itel(nres+2))
1152       itel(:)=0
1153
1154 !      do i=1,2*nres+2
1155 !        do j=1,3
1156 !          c(j,i)=c_alloc(j,i)
1157 !          dc(j,i)=dc_alloc(j,i)
1158 !        enddo
1159 !      enddo
1160 !      do i=1,nres+2
1161 !        itype(i,1)=itype_alloc(i)
1162 !        itel(i)=0
1163 !      enddo
1164 !--------------------------
1165       do i=1,nres
1166 #ifdef PROCOR
1167         if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) then
1168 #else
1169         if (itype(i,1).eq.ntyp1) then
1170 #endif
1171           itel(i)=0
1172 #ifdef PROCOR
1173         else if (iabs(itype(i+1,1)).ne.20) then
1174 #else
1175         else if (iabs(itype(i,1)).ne.20) then
1176 #endif
1177           itel(i)=1
1178         else
1179           itel(i)=2
1180         endif
1181       enddo
1182       if(me.eq.king.or..not.out1file)then
1183        write (iout,*) "ITEL"
1184        print *,nres,"nres"
1185        do i=1,nres-1
1186          write (iout,*) i,itype(i,1),itel(i)
1187        enddo
1188        print *,'Call Read_Bridge.'
1189       endif
1190       call read_bridge
1191 !--------------------------------
1192 !       print *,"tu dochodze"
1193 ! znamy nres oraz nss można zaalokowac potrzebne tablice
1194       call alloc_geo_arrays
1195       call alloc_ener_arrays
1196 !--------------------------------
1197 ! 8/13/98 Set limits to generating the dihedral angles
1198       do i=1,nres
1199         phibound(1,i)=-pi
1200         phibound(2,i)=pi
1201       enddo
1202       read (inp,*) ndih_constr
1203       if (ndih_constr.gt.0) then
1204         raw_psipred=.false.
1205         allocate(idih_constr(ndih_constr),idih_nconstr(ndih_constr)) !(maxdih_constr)
1206         allocate(phi0(ndih_constr),drange(ndih_constr)) !(maxdih_constr)
1207         allocate(ftors(ndih_constr)) !(maxdih_constr)
1208
1209 !        read (inp,*) ftors
1210         read (inp,*) (idih_constr(i),phi0(i),drange(i),ftors(i), &
1211         i=1,ndih_constr)
1212         if(me.eq.king.or..not.out1file)then
1213          write (iout,*) &
1214          'There are',ndih_constr,' constraints on phi angles.'
1215          do i=1,ndih_constr
1216           write (iout,'(i5,3f8.3)') idih_constr(i),phi0(i),drange(i), &
1217           ftors(i)
1218          enddo
1219         endif
1220         do i=1,ndih_constr
1221           phi0(i)=deg2rad*phi0(i)
1222           drange(i)=deg2rad*drange(i)
1223         enddo
1224 !        if(me.eq.king.or..not.out1file) &
1225 !         write (iout,*) 'FTORS',ftors
1226         do i=1,ndih_constr
1227           ii = idih_constr(i)
1228           phibound(1,ii) = phi0(i)-drange(i)
1229           phibound(2,ii) = phi0(i)+drange(i)
1230         enddo
1231       else if (ndih_constr.lt.0) then
1232         raw_psipred=.true.
1233         allocate(idih_constr(nres))
1234         allocate(secprob(3,nres))
1235         allocate(vpsipred(3,nres))
1236         allocate(sdihed(2,nres))
1237         call card_concat(weightcard,.true.)
1238         call reada(weightcard,"PHIHEL",phihel,50.0D0)
1239         call reada(weightcard,"PHIBET",phibet,180.0D0)
1240         call reada(weightcard,"SIGMAHEL",sigmahel,30.0d0)
1241         call reada(weightcard,"SIGMABET",sigmabet,40.0d0)
1242         call reada(weightcard,"WDIHC",wdihc,0.591D0)
1243         write (iout,*) "Weight of dihedral angle restraints",wdihc
1244         read(inp,'(9x,3f7.3)') &
1245           (secprob(1,i),secprob(2,i),secprob(3,i),i=nnt,nct)
1246         write (iout,*) "The secprob array"
1247         do i=nnt,nct
1248           write (iout,'(i5,3f8.3)') i,(secprob(j,i),j=1,3)
1249         enddo
1250         ndih_constr=0
1251         do i=nnt+3,nct
1252           if (itype(i-3,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1 &
1253           .and. itype(i-1,1).ne.ntyp1 .and. itype(i,1).ne.ntyp1) then
1254             ndih_constr=ndih_constr+1
1255             idih_constr(ndih_constr)=i
1256             sumv=0.0d0
1257             do j=1,3
1258               vpsipred(j,ndih_constr)=secprob(j,i-1)*secprob(j,i-2)
1259               sumv=sumv+vpsipred(j,ndih_constr)
1260             enddo
1261             do j=1,3
1262               vpsipred(j,ndih_constr)=vpsipred(j,ndih_constr)/sumv
1263             enddo
1264             phibound(1,ndih_constr)=phihel*deg2rad
1265             phibound(2,ndih_constr)=phibet*deg2rad
1266             sdihed(1,ndih_constr)=sigmahel*deg2rad
1267             sdihed(2,ndih_constr)=sigmabet*deg2rad
1268           endif
1269         enddo
1270
1271       endif
1272       if (with_theta_constr) then
1273 !C with_theta_constr is keyword allowing for occurance of theta constrains
1274       read (inp,*) ntheta_constr
1275 !C ntheta_constr is the number of theta constrains
1276       if (ntheta_constr.gt.0) then
1277 !C        read (inp,*) ftors
1278         allocate(itheta_constr(ntheta_constr))
1279         allocate(theta_constr0(ntheta_constr))
1280         allocate(theta_drange(ntheta_constr),for_thet_constr(ntheta_constr))
1281         read (inp,*) (itheta_constr(i),theta_constr0(i), &
1282        theta_drange(i),for_thet_constr(i), &
1283        i=1,ntheta_constr)
1284 !C the above code reads from 1 to ntheta_constr
1285 !C itheta_constr(i) residue i for which is theta_constr
1286 !C theta_constr0 the global minimum value
1287 !C theta_drange is range for which there is no energy penalty
1288 !C for_thet_constr is the force constant for quartic energy penalty
1289 !C E=k*x**4
1290         if(me.eq.king.or..not.out1file)then
1291          write (iout,*) &
1292         'There are',ntheta_constr,' constraints on phi angles.'
1293          do i=1,ntheta_constr
1294           write (iout,'(i5,3f8.3)') itheta_constr(i),theta_constr0(i), &
1295          theta_drange(i), &
1296          for_thet_constr(i)
1297          enddo
1298         endif
1299         do i=1,ntheta_constr
1300           theta_constr0(i)=deg2rad*theta_constr0(i)
1301           theta_drange(i)=deg2rad*theta_drange(i)
1302         enddo
1303 !C        if(me.eq.king.or..not.out1file)
1304 !C     &   write (iout,*) 'FTORS',ftors
1305 !C        do i=1,ntheta_constr
1306 !C          ii = itheta_constr(i)
1307 !C          thetabound(1,ii) = phi0(i)-drange(i)
1308 !C          thetabound(2,ii) = phi0(i)+drange(i)
1309 !C        enddo
1310       endif ! ntheta_constr.gt.0
1311       endif! with_theta_constr
1312
1313       nnt=1
1314 #ifdef MPI
1315       if (me.eq.king) then
1316 #endif
1317        write (iout,'(a)') 'Boundaries in phi angle sampling:'
1318        do i=1,nres
1319          write (iout,'(a3,i5,2f10.1)') &
1320          restyp(itype(i,1),1),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1321        enddo
1322 #ifdef MP
1323       endif
1324 #endif
1325       nct=nres
1326       print *,'NNT=',NNT,' NCT=',NCT
1327       if (itype(1,molnum(1)).eq.ntyp1_molec(molnum(1))) nnt=2
1328       if (itype(nres,molnum(nres)).eq.ntyp1_molec(molnum(nres))) nct=nct-1
1329       if (pdbref) then
1330         if(me.eq.king.or..not.out1file) &
1331          write (iout,'(a,i3)') 'nsup=',nsup
1332         nstart_seq=nnt
1333         if (nsup.le.(nct-nnt+1)) then
1334           do i=0,nct-nnt+1-nsup
1335             if (seq_comp(itype(nnt+i,1),itype_pdb(nstart_sup),nsup)) then
1336               nstart_seq=nnt+i
1337               goto 111
1338             endif
1339           enddo
1340           write (iout,'(a)') &
1341                   'Error - sequences to be superposed do not match.'
1342           stop
1343         else
1344           do i=0,nsup-(nct-nnt+1)
1345             if (seq_comp(itype(nnt,1),itype_pdb(nstart_sup+i),nct-nnt+1)) &
1346             then
1347               nstart_sup=nstart_sup+i
1348               nsup=nct-nnt+1
1349               goto 111
1350             endif
1351           enddo
1352           write (iout,'(a)') &
1353                   'Error - sequences to be superposed do not match.'
1354         endif
1355   111   continue
1356         if (nsup.eq.0) nsup=nct-nnt
1357         if (nstart_sup.eq.0) nstart_sup=nnt
1358         if (nstart_seq.eq.0) nstart_seq=nnt
1359         if(me.eq.king.or..not.out1file) &
1360          write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,&
1361                        ' nstart_seq=',nstart_seq !,"242343453254"
1362       endif
1363 !--- Zscore rms -------
1364       if (nz_start.eq.0) nz_start=nnt
1365       if (nz_end.eq.0 .and. nsup.gt.0) then
1366         nz_end=nnt+nsup-1
1367       else if (nz_end.eq.0) then
1368         nz_end=nct
1369       endif
1370       if(me.eq.king.or..not.out1file)then
1371        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1372        write (iout,*) 'IZ_SC=',iz_sc
1373       endif
1374 !----------------------
1375       call init_int_table
1376       if (refstr) then
1377         if (.not.pdbref) then
1378           call read_angles(inp,*38)
1379           goto 39
1380    38     write (iout,'(a)') 'Error reading reference structure.'
1381 #ifdef MPI
1382           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1383           stop 'Error reading reference structure'
1384 #endif
1385    39     call chainbuild
1386           call setup_var
1387 !zscore          call geom_to_var(nvar,coord_exp_zs(1,1))
1388           nstart_sup=nnt
1389           nstart_seq=nnt
1390           nsup=nct-nnt+1
1391           kkk=1
1392           do i=1,2*nres
1393             do j=1,3
1394               cref(j,i,kkk)=c(j,i)
1395             enddo
1396           enddo
1397           call contact(.true.,ncont_ref,icont_ref,co)
1398         endif
1399 !        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1400 !        call flush(iout)
1401 !EL        if (constr_dist.gt.0) call read_dist_constr
1402 !EL        write (iout,*) "After read_dist_constr nhpb",nhpb
1403 !EL        if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
1404 !EL        call hpb_partition
1405         if(me.eq.king.or..not.out1file) &
1406          write (iout,*) 'Contact order:',co
1407         if (pdbref) then
1408         if(me.eq.king.or..not.out1file) &
1409          write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1410         do i=1,ncont_ref
1411           do j=1,2
1412             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1413           enddo
1414           if(me.eq.king.or..not.out1file) &
1415            write (2,*) i,' ',restyp(itype(icont_ref(1,i),1),1),' ',&
1416            icont_ref(1,i),' ',&
1417            restyp(itype(icont_ref(2,i),1),1),' ',icont_ref(2,i)
1418         enddo
1419         endif
1420       endif
1421         if (constr_dist.gt.0) call read_dist_constr
1422         write (iout,*) "After read_dist_constr nhpb",nhpb
1423         if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
1424         call hpb_partition
1425
1426       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 &
1427           .and. modecalc.ne.8 .and. modecalc.ne.9 .and. &
1428           modecalc.ne.10) then
1429 ! If input structure hasn't been supplied from the PDB file read or generate
1430 ! initial geometry.
1431         if (iranconf.eq.0 .and. .not. extconf) then
1432           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) &
1433            write (iout,'(a)') 'Initial geometry will be read in.'
1434           if (read_cart) then
1435             read(inp,'(8f10.5)',end=36,err=36) &
1436              ((c(l,k),l=1,3),k=1,nres),&
1437              ((c(l,k+nres),l=1,3),k=nnt,nct)
1438             write (iout,*) "Exit READ_CART"
1439             write (iout,'(8f10.5)') &
1440              ((c(l,k),l=1,3),k=1,nres)
1441             write (iout,'(8f10.5)') &
1442              ((c(l,k+nres),l=1,3),k=nnt,nct)
1443             call int_from_cart1(.true.)
1444             write (iout,*) "Finish INT_TO_CART"
1445             do i=1,nres-1
1446               do j=1,3
1447                 dc(j,i)=c(j,i+1)-c(j,i)
1448                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1449               enddo
1450             enddo
1451             do i=nnt,nct
1452               if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
1453                 do j=1,3
1454                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
1455                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1456                 enddo
1457               endif
1458             enddo
1459             return
1460           else
1461            write(iout,*) "read angles from input"
1462            call read_angles(inp,*36)
1463             call chainbuild
1464
1465           endif
1466           goto 37
1467    36     write (iout,'(a)') 'Error reading angle file.'
1468 #ifdef MPI
1469           call mpi_finalize( MPI_COMM_WORLD,IERR )
1470 #endif
1471           stop 'Error reading angle file.'
1472    37     continue
1473         else if (extconf) then
1474          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0) &
1475           write (iout,'(a)') 'Extended chain initial geometry.'
1476          do i=3,nres
1477           theta(i)=90d0*deg2rad
1478          enddo
1479          do i=4,nres
1480           phi(i)=180d0*deg2rad
1481          enddo
1482          do i=2,nres-1
1483           alph(i)=110d0*deg2rad
1484          enddo
1485          do i=2,nres-1
1486           omeg(i)=-120d0*deg2rad
1487           if (itype(i,1).le.0) omeg(i)=-omeg(i)
1488          enddo
1489          call chainbuild
1490         else
1491           if(me.eq.king.or..not.out1file) &
1492            write (iout,'(a)') 'Random-generated initial geometry.'
1493
1494
1495 #ifdef MPI
1496           if (me.eq.king  .or. fg_rank.eq.0 .and. &
1497                  ( modecalc.eq.12 .or. modecalc.eq.14) ) then
1498 #endif
1499             do itrial=1,100
1500               itmp=1
1501               call gen_rand_conf(itmp,*30)
1502               goto 40
1503    30         write (iout,*) 'Failed to generate random conformation',&
1504                 ', itrial=',itrial
1505               write (*,*) 'Processor:',me,&
1506                 ' Failed to generate random conformation',&
1507                 ' itrial=',itrial
1508               call intout
1509
1510 #ifdef AIX
1511               call flush_(iout)
1512 #else
1513               call flush(iout)
1514 #endif
1515             enddo
1516             write (iout,'(a,i3,a)') 'Processor:',me,&
1517               ' error in generating random conformation.'
1518             write (*,'(a,i3,a)') 'Processor:',me,&
1519               ' error in generating random conformation.'
1520             call flush(iout)
1521 #ifdef MPI
1522             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1523    40       continue
1524           endif
1525 #else
1526           do itrial=1,100
1527             itmp=1
1528             call gen_rand_conf(itmp,*335)
1529             goto 40
1530   335       write (iout,*) 'Failed to generate random conformation',&
1531               ', itrial=',itrial
1532             write (*,*) 'Failed to generate random conformation',&
1533               ', itrial=',itrial
1534           enddo
1535           write (iout,'(a,i3,a)') 'Processor:',me,&
1536             ' error in generating random conformation.'
1537           write (*,'(a,i3,a)') 'Processor:',me,&
1538             ' error in generating random conformation.'
1539           stop
1540    40     continue
1541 #endif
1542         endif
1543       elseif (modecalc.eq.4) then
1544         read (inp,'(a)') intinname
1545         open (intin,file=intinname,status='old',err=333)
1546         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0) &
1547         write (iout,'(a)') 'intinname',intinname
1548         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1549         goto 334
1550   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1551 #ifdef MPI
1552         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1553 #endif
1554         stop 'Error opening angle file.'
1555   334   continue
1556
1557       endif
1558 ! Generate distance constraints, if the PDB structure is to be regularized.
1559       if (nthread.gt.0) then
1560         call read_threadbase
1561       endif
1562       call setup_var
1563       if (me.eq.king .or. .not. out1file) &
1564        call intout
1565       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1566         write (iout,'(/a,i3,a)') &
1567         'The chain contains',ns,' disulfide-bridging cysteines.'
1568         write (iout,'(20i4)') (iss(i),i=1,ns)
1569        if (dyn_ss) then
1570           write(iout,*)"Running with dynamic disulfide-bond formation"
1571        else
1572         write (iout,'(/a/)') 'Pre-formed links are:'
1573         do i=1,nss
1574           i1=ihpb(i)-nres
1575           i2=jhpb(i)-nres
1576           it1=itype(i1,1)
1577           it2=itype(i2,1)
1578           if (me.eq.king.or..not.out1file) &
1579           write (iout,'(2a,i3,3a,i3,a,3f10.3)') &
1580           restyp(it1,1),'(',i1,') -- ',restyp(it2,1),'(',i2,')',dhpb(i),&
1581           ebr,forcon(i)
1582         enddo
1583         write (iout,'(a)')
1584        endif
1585       endif
1586       if (ns.gt.0.and.dyn_ss) then
1587           do i=nss+1,nhpb
1588             ihpb(i-nss)=ihpb(i)
1589             jhpb(i-nss)=jhpb(i)
1590             forcon(i-nss)=forcon(i)
1591             dhpb(i-nss)=dhpb(i)
1592           enddo
1593           nhpb=nhpb-nss
1594           nss=0
1595           call hpb_partition
1596           do i=1,ns
1597             dyn_ss_mask(iss(i))=.true.
1598           enddo
1599       endif
1600       if (i2ndstr.gt.0) call secstrp2dihc
1601       if (indpdb.gt.0) then
1602           write(iout,*) "WCHODZE TU!!"
1603           call int_from_cart1(.true.)
1604       endif
1605 !      call geom_to_var(nvar,x)
1606 !      call etotal(energia(0))
1607 !      call enerprint(energia(0))
1608 !      call briefout(0,etot)
1609 !      stop
1610 !d    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1611 !d    write (iout,'(a)') 'Variable list:'
1612 !d    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1613 #ifdef MPI
1614       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file)) &
1615         write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)') &
1616         'Processor',myrank,': end reading molecular data.'
1617 #endif
1618       return
1619       end subroutine molread
1620 !-----------------------------------------------------------------------------
1621 !-----------------------------------------------------------------------------
1622       end module io