I am trying to simulate contact angle of water on an alpha-quartz slab. I have created an alpha-quartz slab using Avogadro and have the initial coordinates of the atoms. I plan to run energy minimisation of this slab. It would be of great help if someone can outline the procedure of energy minimisation in LAMMPS . It would be great if anyone can share a sample input script related to this.
Minimization is the smallest part of your problem. There is the minimize command, which is documented in the LAMMPS manual and there are links to tutorial material about using LAMMPS on the LAMMPS homepage at Sandia.
The much bigger challenge is to build a suitable topology and assign a force field (and the corresponding parameters and (partial) charges) from having some coordinates. This is very specific to the system at hand and the force field you want to use. There are general explanations of such procedures and how to apply and parameterize force field in molecular modeling text books, which you need to understand first.
No input example can teach you that. There are lots of people at your institution with experience on MD and force field simulations, I suggest reaching out to some of them and arrange for some personal tutoring (best with the help of your supervisor).