Dear all,
I have a .sdf file and wanna make it an input file for lammps, did anybody have some advice?
please note that a) in LAMMPS there is a difference between “input” and “data” file where the former describes the workflow and simulation settings and the latter then geometry, topology and (optionally) the force field assignments.
and b) that for force field calculations you will have to make force field atom type (and bond type etc) assignments which has some force field specific rules and is not something that can be easily automated (even for proteins, where there are large residue/template databases, often some individual tweaks and adjustments are needed).
that said, some tools for pre-processing or converting geometries/topologies are listed here: https://lammps.sandia.gov/prepost.html
for the rest you would need to check with some textbooks and tutorials on MD and force field simulations and carefully study the LAMMPS manual and examples.
axel.