anchor.diff:  c       -2: no result obtained because of negative weights w
   c           or all weights equal to zero.
   cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
  -      subroutine rmsd_score(ndim,nst,w,n_str,Lch,x,y,z,amat,rmsd_delta,
  -     & rmsd_a)
  +      subroutine rmsd_score_all(ndim,nst,w,n_str,Lch,x,y,z,amat,
  +     & rmsd_delta,rmsd_a)
   !     REM: I, J, K, L, M, or N are int
         implicit none
   !     Intent In
  
positive.code:          mark(i)=1
        enddo
        
        if (read_score) then
            call read_score_matrix(nst,n_str,Lch,amat,rmsd_delta,
       &     rmsd_a)
        else
            call rmsd_score(ndim,nst,w,n_str,Lch,x,y,z,amat,rmsd_delta,
       &     rmsd_a)
        endif
  
  ******** reset RMSD_cutoff parameters:
        if(n_para.eq.-1)then      !parameters for ab inito modeling
  
negative.code:       dimension x1(ndim),y1(ndim),z1(ndim),nn1(ndim)
        dimension x2(ndim),y2(ndim),z2(ndim),nn2(ndim)
  
  cjmht
        integer score_type
        logical fcheck
        score_type=0
        fcheck = .FALSE.
  
  **********************************************************************
  ****  check if we are reading a score matrix or processing rmsds
  **********************************************************************
        inquire(file='score.matrix',exist=fcheck)
        if (fcheck) then
            write(*,*)"Scores will be read from file: score.matrix"
            score_type=1
        endif
        inquire(file='TM.score',exist=fcheck)
        if (fcheck) then
            write(*,*)"TM scores will be used"
            if (score_type .ne. 0) then
                write(*,*)'Cannot use score.matrix and TM.score!'
                STOP 1
            endif
            score_type=2
        endif
        if (score_type .eq. 0) then
            write(*,*)"Calculating RMSD scores"
        endif
  
  