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Got it, thanks Rick.

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Yes, I removed those improper lines but after running a simple minimization and that group clash again. Isn't that cause by the missing impropers?

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disa-initialmini.crd.txt (6.58 KB, 790 downloads)
disa-initialmini.pdb.txt (3.74 KB, 790 downloads)
disa-initialmini.psf.txt (15.43 KB, 2721 downloads)
in_glc.out.txt (314.42 KB, 806 downloads)
Initial-minimization_glc.inp.txt (817 Bytes, 805 downloads)
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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.

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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

May I add those torsions?


Thanks again

Attached Images
in_glc.out.txt (8.72 KB, 795 downloads)
create_disa_nhshb.inp.txt (627 Bytes, 778 downloads)
create.out.txt (16.13 KB, 943 downloads)
Initial-minimization_glc.inp.txt (817 Bytes, 798 downloads)
disa.tar.gz (58.95 KB, 741 downloads)
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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.

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