Hello,
I am trying to initialize 2-atom molecules randomly using create_atom.
molecule mols2 mols2.mol
create_atoms 0 random 10 12345 atom_box mol mols2 383
My mols2 file looks like this:
2-atom molecule
2 atoms
1 bonds
0 angles
0 dihedrals
0 impropers
Types
1 1
2 2
Bonds
1 1 1 2
Coords
1 0 0 0
2 0 0 0.97
However, I am getting the error “Bond atoms # # missing at proc # at step #” error. My suspicion is that when I initialize randomly, the second atom is being initialized too far away from the first atom. Is this what is causing this error? If this is indeed the error, how can I prevent this?
Thank you!
Best,
H. Yao