GLYCAM06 has bond types for both S and O2.  Bond length and angle parameters are also included in GLYCAM06.

Make sure you modify the atomic charges for the connecting oxygen atoms according to the following page:
This information is out of date and retained here only for historical purposes. Use the information here at your own risk! These instructions apply to O-sulfation of ...

Xiaocong Wang
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
E-mail: [log in to unmask]

From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Naveen Kumar Vasudevan <[log in to unmask]>
Sent: Thursday, July 13, 2017 3:34:43 PM
To: [log in to unmask]
Subject: Re: SO3 group bond type for GLYCAM in LAMMPS - reg.
No LAMMPS doesn't require specifications for bond order, just requires connectivity information, which I provide via a mol2 file ( it contains bond order). Yes, the partial charges are same it makes sense now, I just wanted to make sure whether the bond types were same or different as per GLYCAM.

Thank you for clarifying my doubt.