I managed to fix the clash by editing the IC entry as you said, tks by the way for all your help. But now two questions arose.
1) There seems to be a problem with the coordinates for the BGLC atoms (this error does not reflect in anything, just annoys me).
CHARMM> read coor univ unit 1 offset 0
SPATIAL COORDINATES BEING READ FROM UNIT 1
** WARNING ** NO COORDINATES FOR 1 1 BGLCA C1
** WARNING ** NO COORDINATES FOR 2 1 BGLCA H1
** WARNING ** NO COORDINATES FOR 3 1 BGLCA O1
** WARNING ** NO COORDINATES FOR 4 1 BGLCA HO1
** WARNING ** NO COORDINATES FOR 5 1 BGLCA C5
2) Where can I find impropers that may match those entries? : No improper parameters for 2 ( SC OC2DP NG2S3 OC2DP )
: No improper parameters for 3 ( NG2S3 SC CC3161 HCP1 )
: No improper parameters for 4 ( SC OC2DP NG2S3 OC2DP )
: A TOTAL OF 3 MISSING PARAMETERS
I will, when done with this parametrization, generate the stream file. Thanks for reminding me that!
All the best