I need to optimize a force field I generated. For this, I should apply Genetic Algorithm (G.A). To apply G.A I should do this for 220 molecules:
1) Find all dihedrals for each molecule ( I did this already with parmchk)
2) Rotate all dihedrals (10-20 degree step in 90 or 360 degree range) and save a mol2 file at each steps.
3) Change all angles (1-2 degree step in 20 or 30 degree range)and save a mol2 file at each step.
Now, I need a program to do this because 220 molecules are too much. I tried "tleap" but it was unstable. I tried pymol but I couldn't run command directly via "cmd" or "terminal" (if there is a way I don't know). So which program should I use?