Odd results from MAN 3 Branched Glycan

[fabgonzal]

Hello, I have had some trouble getting reasonable topologies for branched glycans. For example running with the following fasta and constraints does not produce the correct branching NAG -> NAG -> BMA[branch point] Am I inputting the glycan incorrectly?

FASTA
>protein|motif
GGGNGSGGG
>glycan|Man3
NAG(1-4 NAG(1-4 BMA(1-3 MAN)(1-6 MAN)))

CONSTRAINT
restraint_id,chainA,res_idxA,chainB,res_idxB,connection_type,confidence,min_distance_angstrom,max_distance_angstrom,comment
man3,A,N4@ND2,B,@c1,covalent,1.0,0.0,0.0,toy

[wukevin]

I reformatted your fasta input to reverse the bond ordering as such:

>protein|motif
GGGNGSGGG
>glycan|Man3
NAG(4-1 NAG(4-1 BMA(3-1 MAN)(6-1 MAN)))

and on this branch #234, I'm getting the following structure:

Is this closer to what you are expecting?

[fabgonzal]

Looks good! I see now that the specified bonds are from the previous sugar to the subsequent sugar