Now you're talking! The clash can be relieved by editing the values (especially the dihedral) in the IC C1 C2 N HN entry. I speculate it arose after editing IC C1 C2 N S1 without doing the above. To make the hydrogen "follow" automatically when editing the dihedral associated with the heavy atoms, it is recommended to use an improper IC entry, like this:
IC C2 S1 *N HN 0.0000 0.00 120.00 0.00 0.0000
Where the 120 can be changed to -120 depending on the pyramid flip, and the zeroes can be substituted manually with the correct coordinates, or automatically with IC PARAM.
On an unrelated note:
- You can suppress the charge warning at the beginning of your output by changing the total charge in your topology file like this: PRES AMIN -1.00 .
- It is good practice to leave the main force field files untouched, and make a private self-contained stream file for any additions.
See the CGenFF files and tutorials for examples illustrating all of the above.