anchor.diff:        
   cjmht Calculate the amat with the all-by-all scores
         if (n_para.eq.-2) then
  -          call tm_score_all(ndim,n_str,Lch,x,y,z,amat,rmsd_delta,
  +          call tm_score_all(ndim,nst,n_str,Lch,x,y,z,amat,rmsd_delta,
        &                      rmsd_a)
         elseif (n_para.eq.-3) then
             call read_score_matrix(nst,n_str,amat,rmsd_delta, rmsd_a)
         else
  -          call rmsd_score_all(ndim,w,n_str,Lch,x,y,z,amat,
  +          call rmsd_score_all(ndim,nst,w,n_str,Lch,x,y,z,amat,
        &                        rmsd_delta,rmsd_a)
         endif
   
  
positive.code:       return
        end
  
        subroutine tm_score_all(ndim,n_str,Lch,x,y,z,amat,rmsd_delta,
       &                        rmsd_a)
  c
        implicit none
  
  c     Intent In
        integer ndim
        integer n_str ! Number of structures in use
        integer Lch ! Chain length of the structures (all same)
  c      real x(ndim,nst),y(ndim,nst),z(ndim,nst)
        real, allocatable, intent(in) :: x(:,:),y(:,:), z(:,:)
        real, allocatable, intent(inout) :: amat(:,:)
  c     Intent Out
  c      real amat(nst,nst)
        real rmsd_delta
        double precision rmsd_a
  
  
negative.code:       close(4)
  c^^^^^^^^^^^^^^^^^^^^^^^^ n_str_all done ^^^^^^^^^^^^^^^^^^^^^^^^
  
  cccccccccccc read native structure cccccccccccccccccccc
        i=0
   11   read(3,1239,end=5)tx,ii,tx,tx,ii,tx,a1,a2,a3
  