How to insert R-group(Molecule) in the Scaffold or you can say in root molecule.
For eg. I have root molecule where I have R1, R2 and R3.
How to add specific Molecule in place of R1, R2 and R3 of base molecule.
Reactor is not an R-group enumeration tool, it is a virtual synthesis tool. Please look at the first example on the Reactor documentation page
Please note, that you only need to specify the generic reaction scheme and input files. Reactor will generate all possible products according to the scheme.
If you make use of the reaction rules, your reaction can be chemo-, regio- and stereospecific. It will not generate products from deactivated compounds, and from starting compounds having sensitive functionalities for side reactions. Though designing reaction rules needs same practising, you will be able to generate synthetically feasible products.
(Just a side note: a new Markush Enumeration tool will appear shortly in the upcoming Marvin 5 version. If you have a scaffold with R atoms and all R-groups listed as well, that tool will enumerate for you the members of that library.)