This is a tedious job as a rigid scan as I am unaware of any GUI program that is able to handle a mixed style coordinate input and modification.
DVSA's answer certainly goes into the right direction, but if I'm not mistaken it should perform a (moderedundant) optimisation instead of a scan.
As a start you need to prepare your Cartesian coordinates from your nanotube and insert dummy atoms in strategic places. I am using ChemCraft because it comes with extremely convenient tools. Most importantly in the edit menu there is an entry that lets you insert a dummy atom into the centre of a selected few atoms. Furthermore, you can resymmetrize your molecule later to ensure correct placement.

I placed X (49)
in the centre of C (20)
, C (22)
, C (33)
, C (35)
and directly above X (50)
. In the graphic I marked the coordinates which become most important later in construction. The Cartesian coordinates of X (50)
will later be substituted and become the first line of the z-matrix.
You will need a very good 3D imagination to build the z-matrix from there, or you built the complete model first and measure angles and distances from there.
My anchor atoms will be X (49)
, C (22)
and C (35)
on the nanotube and X (50)
for benzene. To get the alignment right, I am hard-coding the placement of the first carbon into the z-matrix, too. It will be directly above C (35)
.
It is important, that the geometry description block has no blank lines in it. When using the scan
keyword all variables become constants. You will therefore need another block after the geometry specification without any blank lines. If you need to make comments, use !
at the beginning of the line.
The following input will probably do what you want. I have used pm6
as a semiempirical level of theory, because it needed to be quick.
#P pm6
scf(xqc)
scan
benzene nanotube scan
0 1
! 49 Fragment C48X nanotube
C 0.000000000 2.427540000 3.559669000
C 1.196378000 2.072187000 2.878637000
C 2.102311000 1.213770000 3.559669000
C 2.392756000 0.000000000 2.878637000
C 2.102311000 -1.213770000 3.559669000
C 1.196378000 -2.072187000 2.878637000
C 0.000000000 -2.427540000 3.559669000
C -1.196378000 -2.072187000 2.878637000
C -2.102311000 -1.213770000 3.559669000
C -2.392756000 0.000000000 2.878637000
C -2.102311000 1.213770000 3.559669000
C -1.196378000 2.072187000 2.878637000
C -1.196582000 2.072541000 1.430870000
C 0.000000000 2.404111000 0.720134000
C 1.196582000 2.072541000 1.430870000
C 2.082021000 1.202055000 0.720134000
C 2.393165000 0.000000000 1.430870000
C 2.082021000 -1.202055000 0.720134000
C 1.196582000 -2.072541000 1.430870000
C 0.000000000 -2.404111000 0.720134000
C -1.196582000 -2.072541000 1.430870000
C -2.082021000 -1.202055000 0.720134000
C -2.393165000 0.000000000 1.430870000
C -2.082021000 1.202055000 0.720134000
C -2.082021000 1.202055000 -0.720134000
C -1.196582000 2.072541000 -1.430870000
C 0.000000000 2.404111000 -0.720134000
C 1.196582000 2.072541000 -1.430870000
C 2.082021000 1.202055000 -0.720134000
C 2.393165000 0.000000000 -1.430870000
C 2.082021000 -1.202055000 -0.720134000
C 1.196582000 -2.072541000 -1.430870000
C 0.000000000 -2.404111000 -0.720134000
C -1.196582000 -2.072541000 -1.430870000
C -2.082021000 -1.202055000 -0.720134000
C -2.393165000 0.000000000 -1.430870000
C -2.392756000 0.000000000 -2.878637000
C -2.102311000 1.213770000 -3.559669000
C -1.196378000 2.072187000 -2.878637000
C 0.000000000 2.427540000 -3.559669000
C 1.196378000 2.072187000 -2.878637000
C 2.102311000 1.213770000 -3.559669000
C 2.392756000 0.000000000 -2.878637000
C 2.102311000 -1.213770000 -3.559669000
C 1.196378000 -2.072187000 -2.878637000
C 0.000000000 -2.427540000 -3.559669000
C -1.196378000 -2.072187000 -2.878637000
C -2.102311000 -1.213770000 -3.559669000
X -1.041010500 -1.803083000 0.000000000
! 13 Fragment C6H6X benzene
X 49 scan 35 90.000 22 90.000
C 50 xcdist 49 90.000 35 00.000
C 50 xcdist 51 sixty 49 ninety
C 50 xcdist 52 sixty 49 ninety
C 50 xcdist 53 sixty 49 ninety
C 50 xcdist 54 sixty 49 ninety
C 50 xcdist 55 sixty 49 ninety
H 51 chdist 52 onetwen 53 oneeigh
H 52 chdist 53 onetwen 54 oneeigh
H 53 chdist 54 onetwen 55 oneeigh
H 54 chdist 55 onetwen 56 oneeigh
H 55 chdist 56 onetwen 51 oneeigh
H 56 chdist 51 onetwen 52 oneeigh
! 12 Fragment H12 nanotube cappings
H 0.000000000 2.646957000 4.621016000
H 2.292332000 1.323479000 4.621016000
H 2.292332000 -1.323479000 4.621016000
H 0.000000000 -2.646957000 4.621016000
H -2.292332000 -1.323479000 4.621016000
H -2.292332000 1.323479000 4.621016000
H -2.292332000 1.323479000 -4.621016000
H 0.000000000 2.646957000 -4.621016000
H 2.292332000 1.323479000 -4.621016000
H 2.292332000 -1.323479000 -4.621016000
H 0.000000000 -2.646957000 -4.621016000
H -2.292332000 -1.323479000 -4.621016000
scan 2.500 25 0.100
xcdist 1.396
chdist 1.086
sixty 60.000
ninety 90.000
onetwen 120.000
oneeigh 180.000
In my first attempt I forgot the hydrogens so I added them later on. Note that if you change the lines within the Cartesian blocks it does not matter, als long as you don't change the atom numbers of the anchors.
Here is the scan animation of my first attempt (without the hydrogens).

Note that the dummy atoms will be gone in the course of the calculation. Gaussian just needs them to unambiguously define the redundant coordinates.
If you want to run the calculation yourself, you should obtain this table:
Summary of the potential surface scan:
N scan SCF
---- --------- -----------
1 2.5000 1.14872
2 2.6000 1.12058
3 2.7000 1.10061
4 2.8000 1.08668
5 2.9000 1.07712
6 3.0000 1.07067
7 3.1000 1.06641
8 3.2000 1.06365
9 3.3000 1.06192
10 3.4000 1.06088
11 3.5000 1.06030
12 3.6000 1.06001
13 3.7000 1.05990
14 3.8000 1.05990
15 3.9000 1.05996
16 4.0000 1.06004
17 4.1000 1.06013
18 4.2000 1.06022
19 4.3000 1.06030
20 4.4000 1.06037
21 4.5000 1.06043
22 4.6000 1.06048
23 4.7000 1.06052
24 4.8000 1.06055
25 4.9000 1.06057
26 5.0000 1.06059
---- --------- -----------
This whole project would probably be easier solved generating the different geometries by hand.