I am planing to perform a MD simulation of a glycosylated protein (550 amino acid long protein with 6 NAG residues ) in complex with GSH using GROMACS. I wonder if I can ignore these sugars in the MD simulation as they are not in the vicinity of the binding pocket...if not, which considerations should I take into account? Besides, should I treat the GSH as a small ligand (without taking into account that it is actually a peptide?
hi, if the suger has key role in your protein function you can not delete it. Otherwise the suger can be ignored.
Thanks Mokhtar. So if important, how should I proceed? Should I use doGlycans Tool?
Yes!! You shouldn't ignore sugar. You can prepare topology using any tool and I'll suggest please verify the charge of the topology by duing QM calculation (DFT) to get more accurate information.
- Badges
- Science topic