Dear GLYCAM developers and users,
I am interested in simulating a sugar that is acetylated at the 1 position, specifically 1,6-Ac2-alpha-D-Glc, with the GLYCAM forcefield in Amber.
It would appear that there exist no partial charges for this compound (the online builder did not let me place an acetyl derivative at position 1), so I am using the general protocol for deriving the partial charges.
However, in generating the prmtop file using xleap I am encountering the following errors:
** No torsion terms for Os-Cg-Os-C
** No torsion terms for H2-Cg-Os-C
Presumably, GLYCAM is missing the dihedral angle parameters for the O5-C1-O1-C(acetyl) and H1-C1-O1-C(acetyl) dihedral angles.
Can anyone advise a way to overcome this roadblock?
Thank you very much for your help!
Department of Chemistry
University of the Pacific