Dear  List,

 

I have modelled sulphated heparin tetrasaccharide using GLYCAM server. I want to attach lipophilic groups at one of the ends of the tetrasaccharide. Can I use GAFF force-field with AM1/PM3 charges for the lipophilic groups or chain-like (CH2)n? Or am I required to derive RESP charges for the fragment?

 

Your insight is appreciated.

 

Many thanks,

Neha