Nope, it's a (frequently made) mistake in the script that generated the psf file. You need to issue the command "AUTOGENereate ANGLes DIHEdrals" after you're finished patching.
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
I already thought this went a little bit too easy. Yes, all these torsions are required. And validation/optimization would be highly recommended. Especially the C-C-N-S are quite critical.
