SiO2 Nanocluster formation inside a carbonate simulation box

Hello all,

I am new to LAMMPS. I am looking for help with regards to forming a nanocluster of SiO2 inside a box of carbonate molecules. For now I used Material Studio to form the cluster, used the msi2lmp tool to get the moltemplate data file. For less number of molecules its easier to add this data in my Carbonate data file, change the co-ordinates etc according to requirement. But I don’t see a easy way to do it for larger number of molecules(around 5000).
I couldnt not find any option to create a nanocluster data file for moltemplate. This question is more of Moltemplate, but I ll be very thankful if anyone knows any best and easier way to get the nanocluster data along with my carbonate data file (specially the co-ordinates).