I have recently prepared topology, parameter and configuration files for a heparin disaccharide using the GAG builder on the website as follows
Notice that for the irudonic ring I have selected to use the 2S0 configuration. As a result, I get a parm7 and pdb file with the irudonic residue named 2uA2 (instead of the 2uA residue that gets generated for a chair configuration). I want to use tleap to build my system from scratch, without using the parm7 file. Unfortunately, I cannot find the 2uA2 residue anywhere in the prep files that come with amber (or in the glycam webpage). I have noticed that the charges on the atoms is different between 2uA and 2uA2. I was wondering if you could help me find the prep file that is currently used by the GAG builder, so I can use it with tleap.