subroutine readpdb
C Read the PDB file and convert the peptide geometry into virtual-chain 
C geometry.
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'COMMON.LOCAL'
      include 'COMMON.VAR'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.IOUNITS'
      include 'COMMON.GEO'
      include 'COMMON.NAMES'
      include 'COMMON.CONTROL'
      include 'COMMON.DISTFIT'
      include 'COMMON.SETUP'
      character*3 seq,atom,res
      character*80 card
      dimension sccor(3,20)
      double precision e1(3),e2(3),e3(3)
      integer rescode,iterter(maxres),cou
      logical fail
      do i=1,maxres
         iterter(i)=0
      enddo
      ibeg=1
      lsecondary=.false.
      nhfrag=0
      nbfrag=0
      do
        read (ipdbin,'(a80)',end=10) card
        if (card(:5).eq.'HELIX') then
         nhfrag=nhfrag+1
         lsecondary=.true.
         read(card(22:25),*) hfrag(1,nhfrag)
         read(card(34:37),*) hfrag(2,nhfrag)
        endif
        if (card(:5).eq.'SHEET') then
         nbfrag=nbfrag+1
         lsecondary=.true.
         read(card(24:26),*) bfrag(1,nbfrag)
         read(card(35:37),*) bfrag(2,nbfrag)
crc----------------------------------------
crc  to be corrected !!!
         bfrag(3,nbfrag)=bfrag(1,nbfrag)
         bfrag(4,nbfrag)=bfrag(2,nbfrag)
crc----------------------------------------
        endif
        if (card(:3).eq.'END') then
          goto 10
        else if (card(:3).eq.'TER') then
C End current chain
          ires_old=ires+2
          itype(ires_old-1)=ntyp1 
          iterter(ires_old-1)=1
          itype(ires_old)=ntyp1
          iterter(ires_old)=1
          ibeg=2
          write (iout,*) "Chain ended",ires,ishift,ires_old
          if (unres_pdb) then
            do j=1,3
              dc(j,ires)=sccor(j,iii)
            enddo
          else 
            call sccenter(ires,iii,sccor)
          endif
        endif
C Fish out the ATOM cards.
        if (index(card(1:4),'ATOM').gt.0) then  
          read (card(14:16),'(a3)') atom
          if (atom.eq.'CA' .or. atom.eq.'CH3') then
C Calculate the CM of the preceding residue.
            if (ibeg.eq.0) then
              if (unres_pdb) then
                do j=1,3
                  dc(j,ires+nres)=sccor(j,iii)
                enddo
              else
                call sccenter(ires,iii,sccor)
              endif
            endif
C Start new residue.
c            write (iout,'(a80)') card
            read (card(23:26),*) ires
            read (card(18:20),'(a3)') res
            if (ibeg.eq.1) then
              ishift=ires-1
              if (res.ne.'GLY' .and. res.ne. 'ACE') then
                ishift=ishift-1
                itype(1)=ntyp1
              endif
c              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
              ibeg=0          
            else if (ibeg.eq.2) then
c Start a new chain
              ishift=-ires_old+ires-1
c              write (iout,*) "New chain started",ires,ishift
              ibeg=0
            endif
            ires=ires-ishift
c            write (2,*) "ires",ires," ishift",ishift
            if (res.eq.'ACE') then
              itype(ires)=10
            else
              itype(ires)=rescode(ires,res,0)
            endif
            read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
            if(me.eq.king.or..not.out1file)
     &       write (iout,'(2i3,2x,a,3f8.3)') 
     &       ires,itype(ires),res,(c(j,ires),j=1,3)
            iii=1
            do j=1,3
              sccor(j,iii)=c(j,ires)
            enddo
          else if (atom.ne.'O  '.and.atom(1:1).ne.'H' .and. 
     &             atom.ne.'N  ' .and. atom.ne.'C   ') then
            iii=iii+1
            read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
          endif
        endif
      enddo
   10 if(me.eq.king.or..not.out1file) 
     & write (iout,'(a,i5)') ' Nres: ',ires
C Calculate dummy residue coordinates inside the "chain" of a multichain
C system
      nres=ires
      do i=2,nres-1
        write (iout,*) i,itype(i),itype(i+1)
        if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
         if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
           if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
            print *,i,'tu dochodze'
            call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
            if (fail) then
              e2(1)=0.0d0
              e2(2)=1.0d0
              e2(3)=0.0d0
            endif !fail
            print *,i,'a tu?'
            do j=1,3
             c(j,i)=c(j,i-1)-1.9d0*e2(j)
            enddo
           else   !unres_pdb
           do j=1,3
             dcj=(c(j,i-2)-c(j,i-3))/2.0
            if (dcj.eq.0) dcj=1.23591524223
             c(j,i)=c(j,i-1)+dcj
             c(j,nres+i)=c(j,i)
           enddo     
          endif   !unres_pdb
         else     !itype(i+1).eq.ntyp1
          if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the first dummy residue
            call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
            if (fail) then
              e2(1)=0.0d0
              e2(2)=1.0d0
              e2(3)=0.0d0
            endif
            do j=1,3
              c(j,i)=c(j,i+1)-1.9d0*e2(j)
            enddo
          else !unres_pdb
           do j=1,3
            dcj=(c(j,i+3)-c(j,i+2))/2.0
            if (dcj.eq.0) dcj=1.23591524223
            c(j,i)=c(j,i+1)-dcj
            c(j,nres+i)=c(j,i)
           enddo
          endif !unres_pdb
         endif !itype(i+1).eq.ntyp1
        endif  !itype.eq.ntyp1
      enddo
C Calculate the CM of the last side chain.
      if (unres_pdb) then
        do j=1,3
          dc(j,ires)=sccor(j,iii)
        enddo
      else 
        call sccenter(ires,iii,sccor)
      endif
      nsup=nres
      nstart_sup=1
      if (itype(nres).ne.10) then
        nres=nres+1
        itype(nres)=ntyp1
        if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
          call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
          if (fail) then
            e2(1)=0.0d0
            e2(2)=1.0d0
            e2(3)=0.0d0
          endif
          do j=1,3
            c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
          enddo
        else
        do j=1,3
          dcj=(c(j,nres-2)-c(j,nres-3))/2.0
            if (dcj.eq.0) dcj=1.23591524223
          c(j,nres)=c(j,nres-1)+dcj
          c(j,2*nres)=c(j,nres)
        enddo
        endif
      endif
      do i=2,nres-1
        do j=1,3
          c(j,i+nres)=dc(j,i)
        enddo
      enddo
      do j=1,3
        c(j,nres+1)=c(j,1)
        c(j,2*nres)=c(j,nres)
      enddo
      if (itype(1).eq.ntyp1) then
        nsup=nsup-1
        nstart_sup=2
        if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the first dummy residue
          call refsys(2,3,4,e1,e2,e3,fail)
          if (fail) then
            e2(1)=0.0d0
            e2(2)=1.0d0
            e2(3)=0.0d0
          endif
          do j=1,3
            c(j,1)=c(j,2)-1.9d0*e2(j)
          enddo
        else
        do j=1,3
          dcj=(c(j,4)-c(j,3))/2.0
          c(j,1)=c(j,2)-dcj
          c(j,nres+1)=c(j,1)
        enddo
        endif
      endif
C Calculate internal coordinates.
      if(me.eq.king.or..not.out1file)then
       do ires=1,nres
        write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') 
     &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
     &    (c(j,nres+ires),j=1,3)
       enddo
      endif
C      print *,"before int_from_cart"
      call int_from_cart(.true.,.false.)
      call sc_loc_geom(.true.)
      do i=1,nres
        thetaref(i)=theta(i)
        phiref(i)=phi(i)
      enddo
      do i=1,nres-1
        do j=1,3
          dc(j,i)=c(j,i+1)-c(j,i)
          dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
        enddo
      enddo
      do i=2,nres-1
        do j=1,3
          dc(j,i+nres)=c(j,i+nres)-c(j,i)
          dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
        enddo
c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
c     &   vbld_inv(i+nres)
      enddo
c      call chainbuild
C Copy the coordinates to reference coordinates
C Splits to single chain if occurs
      kkk=1
      lll=0
      cou=1
      do i=1,nres
      lll=lll+1
cc      write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
      if (i.gt.1) then
      if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
      chain_length=lll-1
      kkk=kkk+1
c       write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
      lll=1
      endif
      endif
        do j=1,3
          cref(j,i,cou)=c(j,i)
          cref(j,i+nres,cou)=c(j,i+nres)
          if (i.le.nres) then
          chain_rep(j,lll,kkk)=c(j,i)
          chain_rep(j,lll+nres,kkk)=c(j,i+nres)
          endif
         enddo
      enddo
      write (iout,*) chain_length
      if (chain_length.eq.0) chain_length=nres
      do j=1,3
      chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
      chain_rep(j,chain_length+nres,symetr)
     &=chain_rep(j,chain_length+nres,1)
      enddo
c diagnostic
c       write (iout,*) "spraw lancuchy",chain_length,symetr
c       do i=1,4
c         do kkk=1,chain_length
c           write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
c         enddo
c        enddo
c enddiagnostic       
C makes copy of chains
        write (iout,*) "symetr", symetr
       
      if (symetr.gt.1) then
       call permut(symetr)
       nperm=1
       do i=1,symetr
       nperm=nperm*i
       enddo
       do i=1,nperm
       write(iout,*) (tabperm(i,kkk),kkk=1,4)
       enddo
       do i=1,nperm
        cou=0
        do kkk=1,symetr
         icha=tabperm(i,kkk)
c         write (iout,*) i,icha
         do lll=1,chain_length
          cou=cou+1
           if (cou.le.nres) then
           do j=1,3
            kupa=mod(lll,chain_length)
            iprzes=(kkk-1)*chain_length+lll
            if (kupa.eq.0) kupa=chain_length
c            write (iout,*) "kupa", kupa
            cref(j,iprzes,i)=chain_rep(j,kupa,icha)
            cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
          enddo
          endif
         enddo
        enddo
       enddo
       endif
C-koniec robienia kopii
c diag
      do kkk=1,nperm
      write (iout,*) "nowa struktura", nperm
      do i=1,nres
        write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
     &cref(2,i,kkk),
     &cref(3,i,kkk),cref(1,nres+i,kkk),
     &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
      enddo
  100 format (//'              alpha-carbon coordinates       ',
     &          '     centroid coordinates'/
     1          '       ', 6X,'X',11X,'Y',11X,'Z',
     &                          10X,'X',11X,'Y',11X,'Z')
  110 format (a,'(',i3,')',6f12.5)
      
      enddo
cc enddiag
      do j=1,nbfrag     
        do i=1,4                                                       
         bfrag(i,j)=bfrag(i,j)-ishift
        enddo
      enddo

      do j=1,nhfrag
        do i=1,2
         hfrag(i,j)=hfrag(i,j)-ishift
        enddo
      enddo
      return
      end
c---------------------------------------------------------------------------
      subroutine int_from_cart(lside,lprn)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
#ifdef MPI
      include "mpif.h"
#endif 
      include 'COMMON.LOCAL'
      include 'COMMON.VAR'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.IOUNITS'
      include 'COMMON.GEO'
      include 'COMMON.NAMES'
      include 'COMMON.CONTROL'
      include 'COMMON.SETUP'
      character*3 seq,atom,res
      character*80 card
      dimension sccor(3,20)
      integer rescode
      logical lside,lprn
#ifdef MPI
      if(me.eq.king.or..not.out1file)then
#endif
       if (lprn) then 
        write (iout,'(/a)') 
     &  'Internal coordinates calculated from crystal structure.'
        if (lside) then 
          write (iout,'(8a)') '  Res  ','       dvb','     Theta',
     & '       Phi','    Dsc_id','       Dsc','     Alpha',
     & '     Omega'
        else 
          write (iout,'(4a)') '  Res  ','       dvb','     Theta',
     & '       Phi'
        endif
       endif
#ifdef MPI
      endif
#endif
      do i=1,nres-1
        iti=itype(i)
        if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and. 
     &      (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
          write (iout,'(a,i4)') 'Bad Cartesians for residue',i
ctest          stop
        endif
        vbld(i+1)=dist(i,i+1)
        vbld_inv(i+1)=1.0d0/vbld(i+1)
        if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
        if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
      enddo
c      if (unres_pdb) then
c        if (itype(1).eq.21) then
c          theta(3)=90.0d0*deg2rad
c          phi(4)=180.0d0*deg2rad
c          vbld(2)=3.8d0
c          vbld_inv(2)=1.0d0/vbld(2)
c        endif
c        if (itype(nres).eq.21) then
c          theta(nres)=90.0d0*deg2rad
c          phi(nres)=180.0d0*deg2rad
c          vbld(nres)=3.8d0
c          vbld_inv(nres)=1.0d0/vbld(2)
c        endif
c      endif
      print *,"A TU2"
      if (lside) then
        do i=2,nres-1
          do j=1,3
            c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
     &     +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
          enddo
          iti=itype(i)
          di=dist(i,nres+i)
          vbld(i+nres)=di
          if (itype(i).ne.10) then
            vbld_inv(i+nres)=1.0d0/di
          else
            vbld_inv(i+nres)=0.0d0
          endif
          if (iti.ne.10) then
            alph(i)=alpha(nres+i,i,maxres2)
            omeg(i)=beta(nres+i,i,maxres2,i+1)
          endif
          if(me.eq.king.or..not.out1file)then
           if (lprn)
     &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
     &     rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
     &     rad2deg*alph(i),rad2deg*omeg(i)
          endif
        enddo
      else if (lprn) then
        do i=2,nres
          iti=itype(i)
          if(me.eq.king.or..not.out1file)
     &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
     &     rad2deg*theta(i),rad2deg*phi(i)
        enddo
      endif
      return
      end
c-------------------------------------------------------------------------------
      subroutine sc_loc_geom(lprn)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
#ifdef MPI
      include "mpif.h"
#endif 
      include 'COMMON.LOCAL'
      include 'COMMON.VAR'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.IOUNITS'
      include 'COMMON.GEO'
      include 'COMMON.NAMES'
      include 'COMMON.CONTROL'
      include 'COMMON.SETUP'
      double precision x_prime(3),y_prime(3),z_prime(3)
      logical lprn
      do i=1,nres-1
        do j=1,3
          dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
        enddo
      enddo
      do i=2,nres-1
        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
          do j=1,3
            dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
          enddo
        else
          do j=1,3
            dc_norm(j,i+nres)=0.0d0
          enddo
        endif
      enddo
      do i=2,nres-1
        costtab(i+1) =dcos(theta(i+1))
        sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
        cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
        sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
        cosfac2=0.5d0/(1.0d0+costtab(i+1))
        cosfac=dsqrt(cosfac2)
        sinfac2=0.5d0/(1.0d0-costtab(i+1))
        sinfac=dsqrt(sinfac2)
        it=itype(i)
        if (it.ne.10 .and. itype(i).ne.ntyp1) then
c
C  Compute the axes of tghe local cartesian coordinates system; store in
c   x_prime, y_prime and z_prime 
c
        do j=1,3
          x_prime(j) = 0.00
          y_prime(j) = 0.00
          z_prime(j) = 0.00
        enddo
        do j = 1,3
          x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
          y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
        enddo
        call vecpr(x_prime,y_prime,z_prime)
c
C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
C to local coordinate system. Store in xx, yy, zz.
c
        xx=0.0d0
        yy=0.0d0
        zz=0.0d0
        do j = 1,3
          xx = xx + x_prime(j)*dc_norm(j,i+nres)
          yy = yy + y_prime(j)*dc_norm(j,i+nres)
          zz = zz + z_prime(j)*dc_norm(j,i+nres)
        enddo

        xxref(i)=xx
        yyref(i)=yy
        zzref(i)=zz
        else
        xxref(i)=0.0d0
        yyref(i)=0.0d0
        zzref(i)=0.0d0
        endif
      enddo
      if (lprn) then
        do i=2,nres
          iti=itype(i)
#ifdef MPI
          if(me.eq.king.or..not.out1file)
     &     write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
     &      yyref(i),zzref(i)
#else
          write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
     &     zzref(i)
#endif
        enddo
      endif
      return
      end
c---------------------------------------------------------------------------
      subroutine sccenter(ires,nscat,sccor)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'COMMON.CHAIN'
      dimension sccor(3,20)
      do j=1,3
        sccmj=0.0D0
        do i=1,nscat
          sccmj=sccmj+sccor(j,i) 
        enddo
        dc(j,ires)=sccmj/nscat
      enddo
      return
      end
c---------------------------------------------------------------------------
      subroutine bond_regular
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'   
      include 'COMMON.VAR'
      include 'COMMON.LOCAL'      
      include 'COMMON.CALC'
      include 'COMMON.INTERACT'
      include 'COMMON.CHAIN'
      do i=1,nres-1
       vbld(i+1)=vbl
       vbld_inv(i+1)=1.0d0/vbld(i+1)
       vbld(i+1+nres)=dsc(iabs(itype(i+1)))
       vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
c       print *,vbld(i+1),vbld(i+1+nres)
      enddo
      return
      end