I do not have particular specific case but rather a general question about using GLYCAM and GAFF together. I am frequently seeing some ligands, which have a glyacn attached to it (e.g. UDP-GlcNAc, dTDP-Rhanmonse, heparin sulphate etc). I wonder if there is an easy workaround to use GLYCAM for glycan part of the ligand and GAFF for rest of the molecule.
What I was thinking as of now is generate GAFF parameters for the whole molecule and later renaming glycan part (atom names and residue name) to GLYCAM. Missing parameters can be be generated in frcmod file (using parmchk ) ? What I may be missing is parameters for the "connecting bond, angle, dihedral etc".
Have someone tried such a case and can suggest me something ?