subroutine readpdb(lprn,iprot,efree_temp,*)
C Read the PDB file and convert the peptide geometry into virtual-chain 
C geometry.
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.CONTROL'
      include 'COMMON.LOCAL'
      include 'COMMON.VAR'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.IOUNITS'
      include 'COMMON.GEO'
      include 'COMMON.NAMES'
      include 'COMMON.EREF'
      integer i,j,iprot,ibeg,ishift1,ires,iires,iii,ires_old,ishift,ity,
     &  ishift_pdb
      logical lprn,fail
      double precision e1(3),e2(3),e3(3)
      double precision dcj,efree_temp
      character*3 seq,atom,res
      character*80 card,prevcard
      double precision sccor(3,20)
      integer rescode,iterter(maxres)
      efree_temp=0.0d0
      ibeg=1
      ishift1=0
      ishift=0
c      write (iout,*) "READPDB: UNRES_PDB",unres_pdb
c      call flush(iout)
      ires=0
      ires_old=0
      iii=0
      read (ipdbin,'(a80)',end=10) card
      do while (card(:3).eq.'END' .or. card(:3).eq.'TER')
        read (ipdbin,'(a80)',end=10) card
      enddo
      do i=1,10000
         write (iout,'(a)') card
c        call flush(iout)
c        if (card(:3).eq.'END') goto 10
        if (card(:3).eq.'END' .or. 
     &    card(:3).eq.'TER'.and.prevcard(:5).eq.'REMARK') goto 10
        if (card(:3).eq.'TER') then
C End current chain
          write (iout,*) "Im here!"
          write (iout,*) "ires_old",ires_old
          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,*) "ires_old",ires_old
          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
        prevcard=card
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(14:16),'(a3)') atom
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
c          call flush(iout)
          iires=ires-ishift+ishift1
          if (iires.ne.ires_old) then
C Calculate the CM of the preceding residue.
            if (ibeg.eq.0) then
c              write (iout,*) "Calculating sidechain center iii",iii
c              call flush(iout)
              if (unres_pdb) then
                do j=1,3
                  dc(j,ires)=sccor(j,iii)
                enddo
              else
                call sccenter(iires-1,iii,sccor)
              endif
c              write (iout,*) "sidechain center position calculated"
c              call flush(iout)
              iii=0
            endif
C Start new residue.
            if (res.eq.'Cl-' .or. res.eq.'Na+') then
              ires=ires_old
              read (ipdbin,'(a80)',end=10) card
              cycle
            else if (ibeg.eq.1) then
c              write (iout,*) "BEG ires",ires," iires",iires
c              call flush(iout)
              ishift=ires-1
              if (res.ne.'GLY' .and. res.ne. 'ACE') then
                ishift=ishift-1
                itype(1)=ntyp1
              endif
              ires=ires-ishift+ishift1
c              ires_old=ires
c              write (iout,*) "ishift",ishift," ires",ires,
c     &         " iires",iires," ires_old",ires_old
c              call flush(iout)
              ibeg=0          
            else
              ishift=ishift-(ires-ishift+ishift1-ires_old-1)
              ires=ires-ishift+ishift1
c              ires_old=ires
c              write (iout,*) "RESSHIFT",ires,iires,ishift,ishift1
c              call flush(iout)
            endif
c            write (iout,*) "ires",ires," iires",iires
c            call flush(iout)
            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," iires",iires
c          call flush(iout)
          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
c            ishift1=ishift1+1
          endif
c          write (2,*) "iires",iires," 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)
#ifdef DEBUG
            write (iout,'(2i3,2x,a,3f8.3)') 
     &      iires,itype(iires),res,(c(j,ires),j=1,3)
#endif
            iii=iii+1
            do j=1,3
              sccor(j,iii)=c(j,ires)
            enddo
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.ne.'OXT') then
            iii=iii+1
            read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
          endif
        endif
        read (ipdbin,'(a80)',end=10) card
      enddo
   10 write (iout,'(a,i5)') ' Number of residues found: ',ires
      prevcard=card
      if (ires.eq.0) return1
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(iires,iii,sccor)
      endif
      endif
      nres=ires
      nsup(iprot)=nres
      nstart_sup(iprot)=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(iprot)=nsup(iprot)-1
        nstart_sup(iprot)=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,iprot)=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
      call int_from_cart(.true.,lprn)
      call sc_loc_geom(lprn)
c      do i=1,nres
c        phi_ref(i,iprot)=phi(i)
c        theta_ref(i,iprot)=theta(i)
c        alph_ref(i,iprot)=alph(i)
c        omeg_ref(i,iprot)=omeg(i)
c      enddo
      ishift_pdb=ishift
      stop
      return
      end
c---------------------------------------------------------------------------
      subroutine int_from_cart(lside,lprn)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.LOCAL'
      include 'COMMON.VAR'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.IOUNITS'
      include 'COMMON.GEO'
      include 'COMMON.NAMES'
      integer i,j,iti
      double precision dist,alpha,beta,di
      character*3 seq,atom,res
      character*80 card
      double precision sccor(3,20)
      integer rescode
      logical lside,lprn
      if (lprn) then 
        write (iout,'(/a)') 
     &  'Internal coordinates of the reference structure.'
        if (lside) then 
          write (iout,'(8a)') 'Residue','       dvb','     Theta',
     & '       Phi','    Dsc_id','       Dsc','     Alpha',
     & '     Omega'
        else 
          write (iout,'(4a)') 'Residue','       dvb','     Theta',
     & '       Phi'
        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.6.5D0)) then
          write (iout,'(a,i4)') 'Bad Cartesians for residue',i
          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)
        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
      if (lside) then
        do i=2,nct
          do j=1,3
            c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,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
            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
          else
            vbld_inv(i+nres)=0.0d0
            do j=1,3
              dc(j,i+nres)=0.0d0
              dc_norm(j,i+nres)=0.0d0
            enddo
          endif
          if (iti.ne.10) then
            alph(i)=alpha(nres+i,i,maxres2)
            omeg(i)=beta(nres+i,i,maxres2,i+1)
          endif
          if (lprn)
     &    write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
     &    rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,
     &    rad2deg*alph(i),rad2deg*omeg(i)
          if (iti.ne.10) then
          endif
        enddo
      else if (lprn) then
        do i=2,nres
          iti=itype(i)
          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'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.LOCAL'
      include 'COMMON.VAR'
      include 'COMMON.CHAIN'
      include 'COMMON.INTERACT'
      include 'COMMON.IOUNITS'
      include 'COMMON.GEO'
      include 'COMMON.NAMES'
      include 'COMMON.CONTROL'
      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

        xxtab(i)=xx
        yytab(i)=yy
        zztab(i)=zz
        else
        xxtab(i)=0.0d0
        yytab(i)=0.0d0
        zztab(i)=0.0d0
        endif
      enddo
      if (lprn) then
        do i=2,nres
          iti=itype(i)
          write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxtab(i),yytab(i),
     &     zztab(i)
        enddo
      endif
      return
      end
c---------------------------------------------------------------------------
      subroutine sccenter(ires,nscat,sccor)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.CHAIN'
      integer ires,nscat,i,j
      double precision sccmj
      double precision 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