I'm sorry,

I ran it before with BOMLEV 0 but wanted to test whether it would work with -3.

That's how the script ends with BOMLEV 0

CHARMM> patch amin S 2 setup
ATOM S 2 AGLCNA C AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA O AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA CT AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA HT1 AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA HT2 AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA HT3 AND ALL REFERENCES TO IT DELETED.
ATOM S AGLCNA 2 S ADDED.
ATOM S AGLCNA 2 O2 ADDED.
ATOM S AGLCNA 2 O7 ADDED.
ATOM S AGLCNA 2 O8 ADDED.

Message from MAPIC: Atom numbers are changed.
DELTIC: 6 bonds deleted
DELTIC: 11 angles deleted
DELTIC: 13 dihedrals deleted
DELTIC: 2 improper dihedrals deleted
*** LEVEL -3 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.

ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -3

Attached Images
create_disa_nhshb.inp.txt (594 Bytes, 826 downloads)
nhshb.out.txt (6.82 KB, 854 downloads)