Dear experts, I am a new learner of Perl. I want extract some information from my output files of my calculations. I have written the following script:

#!/usr/bin/perl
# 2017.02.07
# Compare Qc and Dc of gold atoms
use strict;

open(F1,">SI.txt");
open(F2,">SI2.txt");
print F2 "\n\n\n============================
Computed geometries (Cartesian coordinates in Angstrom), total energie
+s (Hartree),
Hirshfeld population  QA(e) and atomic overlap distances DA(bohr) of a
+ll systems
given in Table SI-1 and Table SI-2. \n\n";

print F1 "\n\n\n==========================
Computed Q(Au) and D(Au) of all atoms in all neutral Au clusters \n\n"
+;

print F1 "   Atom      QA       DA(alpha)   DA(beta)    DA(total)\n";
foreach my $f(<*log>){
        my $c=`grep -c "Normal term" $f`;chomp($c);
        my $E=`tac $f|grep -m1 "SCF Done"|awk "{print \\\$5}"`; chomp(
+$E);
        my $Nat = `cat $f|grep -m1 "NAtoms="|awk "{print \\\$2}" `; ch
+omp($Nat);
                my $off=$Nat+4;
                my $coord=`tac $f|grep -m1 -B$off " orientation:"|head
+ -n$Nat|tac|awk -v OFS='\t' "{print\\\$1,\\\$2,\\\$4,\\\$5,\\\$6}"`;
                print F2 "Molecule $f \nEnergy: $E\nGeometry:\nAtom  A
+tomic No.   x                 y               z\n $coord   Atom      
+QA       DA(alpha)   DA(beta)    DA(total)\n";
                foreach my $at(1..$Nat){
                        my $at2=$at+1;

                        # Get the Hirshfeld populations and atomic del
+ocalziations
                        my $QA = `tac $f|grep -m1 -B$at2 "Hirshfeld ch
+arges, spin" | head -n1|awk "{print \\\$3}"`;chomp($QA);
                        my $dalpha=`tac $f|grep -m1 -B$at2 "Atomic ave
+rage delocal" |head -n1 |awk "{print \\\$3}"`; chomp($dalpha);
                        my $dbeta=`tac $f|grep -m1 -B$at2 "Atomic aver
+age delocal" |head -n1 |awk "{print \\\$4}"`; chomp($dbeta);
                        my $dtotal=`tac $f|grep -m1 -B$at2 "Atomic ave
+rage delocal" |head -n1 |awk "{print \\\$5}"`; chomp($dtotal);
                        print F1 sprintf(" %4d     %7.4f     %7.4f    
+ %7.4f     %7.4f \n",$at,$QA,$dalpha,$dbeta,$dtotal);
                }
        }
close(F1);
close(F2);
[download]

Using my limited knowledge of Perl, I have successfully extracted what I want from my output files in two files SI.txt and SI2.txt. But I want to combine information about each molecule in one file. I don't know how to write script that combines the information into one file. File SI.txt gives me:

   Atom      QA       DA(alpha)   DA(beta)    DA(total)
    1      1.0000      2.2238      2.6173      2.3812
    1      1.3294      1.9996      1.9996      1.9996
    2     -0.1098      2.2233      2.2233      2.2233
    3     -0.1098      2.2233      2.2233      2.2233
    4     -0.1098      2.2233      2.2233      2.2233
[download]

and File SI2.txt gives me:

Molecule 01-Carbon-Energy.log
Energy: -37.7131454546
Geometry:
Atom  Atomic No.   x                y               z
 1      6       0.000000        0.000000        0.000000
   Atom      QA       DA(alpha)   DA(beta)    DA(total)
Molecule 02-Methanide-Geometry.log
Energy: -39.6946868929
Geometry:
Atom  Atomic No.   x                y               z
 1      6       0.000000        0.000000        0.000000
2       1       0.000000        1.084453        0.000000
3       1       -0.939164       -0.542227       0.000000
4       1       0.939164        -0.542227       0.000000
   Atom      QA       DA(alpha)   DA(beta)    DA(total)
[download]

But this is what I want:

Molecule 01-Carbon-Energy.log
Energy: -37.7131454546
Geometry:
Atom  Atomic No.   x                y               z
 1      6       0.000000        0.000000        0.000000
   Atom      QA       DA(alpha)   DA(beta)    DA(total)
    1      1.0000      2.2238      2.6173      2.3812
Molecule 02-Methanide-Geometry.log
Energy: -39.6946868929
Geometry:
Atom  Atomic No.   x                y               z
 1      6       0.000000        0.000000        0.000000
2       1       0.000000        1.084453        0.000000
3       1       -0.939164       -0.542227       0.000000
4       1       0.939164        -0.542227       0.000000
   Atom      QA       DA(alpha)   DA(beta)    DA(total)
    1      1.3294      1.9996      1.9996      1.9996
    2     -0.1098      2.2233      2.2233      2.2233
    3     -0.1098      2.2233      2.2233      2.2233
    4     -0.1098      2.2233      2.2233      2.2233
[download]

Please help me, if possible. I shall be very much thankful