Carbohydrates
Martini 2 parameters for some carbohydrates developed by the Martini community over the years are listed below with some usage clarifications and references for further description of these works.
Martini 2.2 N-Glycans
Topologies for Martini 2.2 glycans are available for download here, courtesy of César López Bautista and co-workers. For further background reading, please see:
- S. Chakraborty, K. Wagh, S. Gnanakaran, C. A. López. Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics. Glycobiology, (doi: 10.1093/glycob/cwab017)
Common mono-/di-saccharides, and amylose.
Topologies for Martini 2 mono-/di-saccharides and amylose are available for download here. For further background reading, please see:
- C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Hunenberger, S.J. Marrink. The MARTINI coarse-grained force field: Extension to carbohydrates JCTC, (doi: 10.1021/ct900313w)
Beta-cyclodextrin, Dimethyl-cyclodextrin and Hydroxypropyl-cyclodextrin
Topologies for Martini 2 beta-cyclodextrin, dimethyl-cyclodextrin and hydroxypropyl-cyclodextrin are available for download here. A new bead type must be incorporated for beta cyclodextrin, which is included in the martini_v2.1_pc.itp file. Beta cyclodextrin is represented as a dimer, since it is the prevalent type in solution. However it can be easily transformed into a monomer if necessary. For further background reading, please see:
- López, C. A., de Vries, A. H., & Marrink, S. J. Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Scientific Reports, (doi: 10.1038/srep02071)