In TraPPE force field, all alkyl groups and functional groups are treated as semiflexible with fixed bond lengths but bending and torsional degrees of freedom. Rigid bonds can be realized in LAMMPS with fix shake. But there would be en error reminding me that ‘fix shake clusters are connected’ when I try to constrain the three bonds in TraPPE-UA n-butane molecules. Is there a way to use TraPPE-UA n-butane model in LAMMPS? Any suggestion could help, thanks.

I am not aware of a way to make this work in LAMMPS (and most MD codes).
The TraPPE force fields were designed for Monte Carlo simulations, where enforcing bond lengths is very simple since you always do one move at a time. In MD this is different and solving the SHAKE constraint equations is very complicated since you are moving all atoms at the same time.

There are three possible workarounds:

you can leave the bonds flexible, but use a very strong force constant. That will require you reduce your time step and even then, your bond lengths will only be approximate, so you are not fully compliant with the force field

you can use the POEMS package in LAMMPS and define each bond as a rigid object. The POEMS solver is supposed to have solutions for connected rigid objects, but I am not certain whether it can handle such a massive system. You will also need to reduce the time step, parallel efficiency will drop, and creating the input will be messy.

you can switch to a different force field that does not have the restriction