Shell Programming and Scripting

#!/usr/bin/awk

      BEGIN { s=0;n=0 }
                   { n++; s=s+(($n)^2-($50)^2) }
      END
      { print sqrt(s/50) }

2.91187 4.25656 7.3225   ..... until column 50 
3.4187   2.67656 6.3225
3.54117 6.27656 4.3225
5.61187 6.27656 2.3225
....          ...           ....

RMSD
4.31185 
3.4185   
2.64115
4.71183 
....

awk -f rmsd merge.pmf 
awk: syntax error at source line 6 source file rmsd
 context is
          END  >>> 
 <<< 
awk: bailing out at source line 7

NF {    LINE++; MAX=NF; for(N=1; N<=NF; N++) A[LINE,N]=$N       }
END     {
        # Calculate sum for each column and row
        for(COL=1; COL<=MAX; COL++)
        for(ROW=1; ROW<=LINE; ROW++)
                AVG[COL]+=A[ROW,COL];

        # Turn the sums into averages
        for(COL=1; COL<=MAX; COL++) AVG[COL] /= LINE

        # Calculate deviations for each column and row
        for(COL=1; COL<=MAX; COL++)
        for(ROW=1; ROW<=LINE; ROW++)
                DEV[COL]+=(AVG[COL]-A[ROW,COL])^2

        # Divide sum by number of lines, then give the square root.
        for(COL=1; COL<=MAX; COL++)     print sqrt(DEV[COL]/LINE);
}

2.91187  2.27656  3.3225  2.33938 2.55781 3.05656 2.66063 2.02781... ... 2.31219

set mean  = `awk '{++n;sum+=$NF} END{if(n) print sum/n}' slice.txt`

set rmsd  = `awk -v mean=$mean '{++n;sum+=($NF-mean)^2} END{if(n) print sqrt(sum/n)}' slice.txt`