Update several scripts and add a new script for generating topology files

[yskmiyazaki]

updated files

• bin/cg_spica : due to the update json_to_top.py
• src/setup_lmp.py : make use of dihedral hybrid style for impropers
• src/setup_gmx.py : remove duplicated included itp files in topol.top
• gen_lmp_input.py : add an index variable dt to easily control the timestep in a command-line
• json_to_top.py : add functions to output manually defined angle, dihedral, and improper lists in spica json files
• spica_top.json : remove some molecule information that is not used