Gmml will accept the above string and build a structure for it. Amber will minimize it:
Gmml should instead detect that the structure isn't feasible throw an error. The residue codes protect us from this in other cases like this:
DGlcpa1-3[DGlcpa1-3]DGlcpa1-OH, where we get the error:
No linkage code found in GMML metadata for a carbohydrate residue with other residues attached at these positions: 3,3
But the anomeric position is treated differently.
Gmml will accept the above string and build a structure for it. Amber will minimize it:
Gmml should instead detect that the structure isn't feasible throw an error. The residue codes protect us from this in other cases like this:
DGlcpa1-3[DGlcpa1-3]DGlcpa1-OH, where we get the error:
No linkage code found in GMML metadata for a carbohydrate residue with other residues attached at these positions: 3,3
But the anomeric position is treated differently.