anchor.diff:        dist = sqrt(dist)
         return
         end function
  +
         subroutine my_get_command_argument(i,buffer,l,istatus)
         implicit none
         integer i
  
positive.code:        integer, dimension(:), allocatable :: im
         integer, dimension(:,:), allocatable :: p2
         integer, dimension(:,:), allocatable :: p3
         character*16 , dimension(:), allocatable :: ta,tr
         integer i
         integer n2
   
  c
         call smd_pdb_natoms(infile,ntot)
  
negative.code:       do j=i+1,nres
          r2 = cg(:,j)
          rd  = dist(r1,r2)
          if(rd.lt.3.0) then
            k = k + 1
            p2(1,k) = i
  