Dear Rob and Oliver, 

Thank you so much for your helps and suggestions.

Yes, I use the gag builder tool to build the heparin but first I have the problems about the naming and parameters of some residues (e.g. (UYS, QYS, and 6YS) that parameter of these residues cannot be found in  GLYCAM_06j-1.prep and leaprc.GLYCAM_06j-1. Then, I use the updated glycam parameters (leaprc.GLYCAM_06k and GLYCAM_06k.prep) and parameters of these residues can be found in these new parameter files (leaprc.GLYCAM_06k and GLYCAM_06k.prep). However, I got another problems that the total charge is not 0. But I can solve the problems now. 

Just follow the tutorial as suggested by Oliver ( To summarize, I just have to change the charge of oxygen atom of the residue that is connected to the sulfate group by adding this value (+0.031) to the original value provided in the  GLYCAM_06k.prep. Then, finally I have a heparin with the total charge is integer and equal to 0 after adding counter ions. 

Thank you very much,
Kanin Wichapong