Thanks for the answer and sorry for being such a novice, but now when trying to minimize I get this error:
CHARMM> energy
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec FSWItch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 946 atom pairs and 264 atom exclusions. There are 0 group pairs and 23 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1082 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found: 946 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES
: No torsion parameters for 72 ( CC3162 CC3161 NG2S3 SC ) : No torsion parameters for 101 ( CC3161 NG2S3 SC OC2DP ) : No torsion parameters for 102 ( CC3161 NG2S3 SC OC2DP ) : No torsion parameters for 103 ( CC3161 NG2S3 SC OC2DP ) : No torsion parameters for 108 ( HCA1 CC3161 NG2S3 SC ) : No torsion parameters for 116 ( HCP1 NG2S3 SC OC2DP ) : No torsion parameters for 117 ( HCP1 NG2S3 SC OC2DP ) : No torsion parameters for 118 ( HCP1 NG2S3 SC OC2DP ) : No torsion parameters for 119 ( SC NG2S3 CC3161 CC3161 ) : A TOTAL OF 9 MISSING PARAMETERS
***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5