(It may help:Using VESTA)

1) Import graphene cif file in VESTA.

2) Edit>unit-cell>structural parameters>add/remove atoms.

3) Then add the atomic positions of the atoms (of the molecule) above the graphene surface.

(most important step)

4) select apply.

5) Examine it carefully in terms of bond lengths, etc.

6) if every step is OK, export it as cif and open it in MS for CASTEP run.

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All this can also be done manually in MS for CASTEP by looking for "relevant options".