I’m currently trying to simulate a 4 molecule system. Each molecule has around 170 atoms, so I’m using moltemplate to join the datafiles and generate a lammps input file which includes all the molecules with their corresponding force field coefficients. I have been using the Itemplify.py script to generate the .lt files for each molecule, but when I try to run moltemplate.sh , the final file doesn’t include the pair, bond , angle and dihedral coeffs required for running the simulation.
I have specified the “inherits oplsaa” in the Itemplify.py script. I have tried running it with several combinations of flags (ignore-coeffs, ignore-angles, ignore-bond types, etc). I have also made sure the import “oplsaa.lt” is included in the final .lt files, but still haven’t been able to make moltemplate calculate the coefficients. I there something I’m missing ?
thanks a lot for your time