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'
      include 'COMMON.FRAG'
      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
     &  ishift_pdb
      logical lprn /.false./,fail
      double precision e1(3),e2(3),e3(3)
      double precision dcj,efree_temp
      character*3 seq,res
      character*5 atom
      character*80 card
      double precision sccor(3,50)
      integer rescode
      efree_temp=0.0d0
      ibeg=1
      ishift1=0
      ishift=0
c      write (2,*) "UNRES_PDB",unres_pdb
      ires=0
      ires_old=0
      iii=0
      lsecondary=.false.
      nhfrag=0
      nbfrag=0
      do
        read (ipdbin,'(a80)',end=10) card
c        write (iout,'(a)') 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' .or. card(:3).eq.'TER') goto 10
c Read free energy
        if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
C Fish out the ATOM cards.
        if (index(card(1:4),'ATOM').gt.0) then  
          read (card(12:16),*) atom
c          write (iout,*) "! ",atom," !",ires
c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
          read (card(23:26),*) ires
          read (card(18:20),'(a3)') res
c          write (iout,*) "ires",ires,ires-ishift+ishift1,
c     &      " ires_old",ires_old
c          write (iout,*) "ishift",ishift," ishift1",ishift1
c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
          if (ires-ishift+ishift1.ne.ires_old) then
C Calculate the CM of the preceding residue.
c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
            if (ibeg.eq.0) then
c              write (iout,*) "Calculating sidechain center iii",iii
              if (unres_pdb) then
                do j=1,3
                  dc(j,ires)=sccor(j,iii)
                enddo
              else
                call sccenter(ires_old,iii,sccor)
              endif
              iii=0
            endif
C Start new residue.
            if (res.eq.'Cl-' .or. res.eq.'Na+') then
              ires=ires_old
              cycle
            else if (ibeg.eq.1) then
c              write (iout,*) "BEG ires",ires
              ishift=ires-1
              if (res.ne.'GLY' .and. res.ne. 'ACE') then
                ishift=ishift-1
                itype(1)=ntyp1
              endif
              ires=ires-ishift+ishift1
              ires_old=ires
c              write (iout,*) "ishift",ishift," ires",ires,
c     &         " ires_old",ires_old
              ibeg=0          
            else
              ishift=ishift-(ires-ishift+ishift1-ires_old-1)
              ires=ires-ishift+ishift1
              ires_old=ires
            endif
            if (res.eq.'ACE' .or. res.eq.'NHE') then
              itype(ires)=10
            else
              itype(ires)=rescode(ires,res,0)
            endif
          else
            ires=ires-ishift+ishift1
          endif
c          write (iout,*) "ires_old",ires_old," ires",ires
          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
c            ishift1=ishift1+1
          endif
c          write (2,*) "ires",ires," res ",res," ity",ity
          if (atom.eq.'CA' .or. atom.eq.'CH3' .or. 
     &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
            read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
c            write (iout,*) "backbone ",atom 
#ifdef DEBUG
            write (iout,'(2i3,2x,a,3f8.3)') 
     &      ires,itype(ires),res,(c(j,ires),j=1,3)
#endif
            iii=iii+1
            do j=1,3
              sccor(j,iii)=c(j,ires)
            enddo
            if (ishift.ne.0) then
              ires_ca=ires+ishift-ishift1
            else
              ires_ca=ires
            endif
c            write (*,*) card(23:27),ires,itype(ires)
          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
     &             atom.ne.'N' .and. atom.ne.'C' .and.
     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
     &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
c            write (iout,*) "sidechain ",atom
            iii=iii+1
            read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
          endif
        endif
      enddo
   10 continue
#ifdef DEBUG
      write (iout,'(a,i5)') ' Number of residues found: ',ires
#endif
      if (ires.eq.0) return
C Calculate the CM of the last side chain.
      if (iii.gt.0)  then
      if (unres_pdb) then
        do j=1,3
          dc(j,ires)=sccor(j,iii)
        enddo
      else
        call sccenter(ires,iii,sccor)
      endif
      endif
      nres=ires
      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)-3.8d0*e2(j)
          enddo
        else
        do j=1,3
          dcj=c(j,nres-2)-c(j,nres-3)
          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)-3.8d0*e2(j)
          enddo
        else
        do j=1,3
          dcj=c(j,4)-c(j,3)
          c(j,1)=c(j,2)-dcj
          c(j,nres+1)=c(j,1)
        enddo
        endif
      endif
C Copy the coordinates to reference coordinates
c      do i=1,2*nres
c        do j=1,3
c          cref(j,i)=c(j,i)
c        enddo
c      enddo
C Calculate internal coordinates.
      if (lprn) then
      write (iout,'(/a)') 
     &  "Cartesian coordinates of the reference structure"
      write (iout,'(a,3(3x,a5),5x,3(3x,a5))') 
     & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
      do ires=1,nres
        write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') 
     &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
     &    (c(j,ires+nres),j=1,3)
      enddo
      endif
C Calculate internal coordinates.
      if(me.eq.king.or..not.out1file)then
       write (iout,'(a)') 
     &   "Backbone and SC coordinates as read from the PDB"
       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
      call int_from_cart(.true.,.false.)
      call sc_loc_geom(.false.)
      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
      do i=1,2*nres
        do j=1,3
          cref(j,i)=c(j,i)
        enddo
      enddo


      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
      ishift_pdb=ishift
      return
      end
c-----------------------------------------------------------------------
      subroutine readpdb_template(k)
C Read the PDB file with gaps for read_constr_homology with read2sigma
C and convert the peptide geometry into virtual-chain 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'
      include 'COMMON.MD'
      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
     &  ishift_pdb
      logical lprn /.false./,fail
      double precision e1(3),e2(3),e3(3)
      double precision dcj,efree_temp
      character*3 seq,res
      character*5 atom
      character*80 card
      double precision sccor(3,50)
      integer rescode
      efree_temp=0.0d0
      ibeg=1
      ishift1=0
      ishift=0
c      write (2,*) "UNRES_PDB",unres_pdb
      ires=0
      ires_old=0
      iii=0
      lsecondary=.false.
      nhfrag=0
      nbfrag=0
      do 
        read (ipdbin,'(a80)',end=10) card
c        write (iout,'(a)') card
        if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
C Fish out the ATOM cards.
        if (index(card(1:4),'ATOM').gt.0) then  
          read (card(12:16),*) atom
c          write (iout,*) "! ",atom," !",ires
c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
          read (card(23:26),*) ires
          read (card(18:20),'(a3)') res
c          write (iout,*) "ires",ires,ires-ishift+ishift1,
c     &      " ires_old",ires_old
c          write (iout,*) "ishift",ishift," ishift1",ishift1
c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
          if (ires-ishift+ishift1.ne.ires_old) then
C Calculate the CM of the preceding residue.
c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
            if (ibeg.eq.0) then
c              write (iout,*) "Calculating sidechain center iii",iii
              if (unres_pdb) then
                do j=1,3
                  dc(j,ires)=sccor(j,iii)
                enddo
              else
                call sccenter(ires_old,iii,sccor)
              endif
              iii=0
            endif
C Start new residue.
            if (res.eq.'Cl-' .or. res.eq.'Na+') then
              ires=ires_old
              cycle
            else if (ibeg.eq.1) then
c              write (iout,*) "BEG ires",ires
              ishift=ires-1
              if (res.ne.'GLY' .and. res.ne. 'ACE') then
                ishift=ishift-1
                itype(1)=ntyp1
              endif
              ires=ires-ishift+ishift1
              ires_old=ires
c              write (iout,*) "ishift",ishift," ires",ires,
c     &         " ires_old",ires_old
              ibeg=0          
            else
              ishift=ishift-(ires-ishift+ishift1-ires_old-1)
              ires=ires-ishift+ishift1
              ires_old=ires
            endif
            if (res.eq.'ACE' .or. res.eq.'NHE') then
              itype(ires)=10
            else
              itype(ires)=rescode(ires,res,0)
            endif
          else
            ires=ires-ishift+ishift1
          endif
c          write (iout,*) "ires_old",ires_old," ires",ires
          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
c            ishift1=ishift1+1
          endif
c          write (2,*) "ires",ires," res ",res," ity",ity
          if (atom.eq.'CA' .or. atom.eq.'CH3' .or. 
     &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
            read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
c            write (iout,*) "backbone ",atom 
#ifdef DEBUG
            write (iout,'(2i3,2x,a,3f8.3)') 
     &      ires,itype(ires),res,(c(j,ires),j=1,3)
#endif
            iii=iii+1
            do j=1,3
              sccor(j,iii)=c(j,ires)
            enddo
            if (ishift.ne.0) then
              ires_ca=ires+ishift-ishift1
            else
              ires_ca=ires
            endif
c            write (*,*) card(23:27),ires,itype(ires)
          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
     &             atom.ne.'N' .and. atom.ne.'C' .and.
     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
     &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
c            write (iout,*) "sidechain ",atom
            iii=iii+1
            read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
          endif
        endif
      enddo
   10 continue
#ifdef DEBUG
      write (iout,'(a,i5)') ' Number of residues found: ',ires
#endif
      if (ires.eq.0) return
C Calculate the CM of the last side chain.
      if (iii.gt.0)  then
      if (unres_pdb) then
        do j=1,3
          dc(j,ires)=sccor(j,iii)
        enddo
      else
        call sccenter(ires,iii,sccor)
      endif
      endif
      nres=ires
      nsup=nres
      nstart_sup=1
      if (itype(nres).ne.10) then
        nres=nres+1
        itype(nres)=ntyp1
        do j=1,3
          dcj=c(j,nres-2)-c(j,nres-3)
          c(j,nres)=c(j,nres-1)+dcj
          c(j,2*nres)=c(j,nres)
        enddo
      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)-3.8d0*e2(j)
          enddo
        else
        do j=1,3
          dcj=c(j,4)-c(j,3)
          c(j,1)=c(j,2)-dcj
          c(j,nres+1)=c(j,1)
        enddo
        endif
      endif
C Calculate internal coordinates.
      if (lprn) then
      write (iout,'(/a)') 
     &  "Cartesian coordinates of the reference structure"
      write (iout,'(a,3(3x,a5),5x,3(3x,a5))') 
     & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
      do ires=1,nres
        write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') 
     &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
     &    (c(j,ires+nres),j=1,3)
      enddo
      endif
C Calculate internal coordinates.
      if(me.eq.king.or..not.out1file)then
       write (iout,'(a)') 
     &   "Backbone and SC coordinates as read from the PDB"
       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
      call int_from_cart(.true.,.false.)
      call sc_loc_geom(.false.)
      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
      do i=1,2*nres
        do j=1,3
          cref(j,i)=c(j,i)
          chomo(j,i,k)=c(j,i)
        enddo
      enddo


      ishift_pdb=ishift
      return
      end