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disaccharide and oligosaccharides of glucose
- aelahi4
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3 years 2 weeks ago #8909
by aelahi4
disaccharide and oligosaccharides of glucose was created by aelahi4
Hi all
Sorry in advance if my questions are very rudimentary as I'm partially new to this field.
I'm using this reference to construct CG beads representing glucose polysaccharides.
"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, 5:3195-3210, 2009."
and I have following questions:
1- based on the images, I could not figure out what these atoms belong to
O1, O5 , O4 (for both isomers) and glycosidic oxygen. this is my guess:
B2: glycosidic-O, C1,C4 and O4
B4: O1, C1, C4 and glycosidic-O
so does glycosidic-O belong to both B2 and B4?
3- Is there any reason why some angles are not parameterized? e.g., B1-B2-B3
4- Can this basis glucose model be used for CG model construction of cellulose derivatives. e.g., ethyl cellulose? If yes, I couldn't find ethyl group (2:1) mapping parameters, except one in the tutorial that used TP5. Can I use the same, or should I redo parameterization?
Thank you very much for your response
Sorry in advance if my questions are very rudimentary as I'm partially new to this field.
I'm using this reference to construct CG beads representing glucose polysaccharides.
"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, 5:3195-3210, 2009."
and I have following questions:
1- based on the images, I could not figure out what these atoms belong to
O1, O5 , O4 (for both isomers) and glycosidic oxygen. this is my guess:
B2: glycosidic-O, C1,C4 and O4
B4: O1, C1, C4 and glycosidic-O
so does glycosidic-O belong to both B2 and B4?
3- Is there any reason why some angles are not parameterized? e.g., B1-B2-B3
4- Can this basis glucose model be used for CG model construction of cellulose derivatives. e.g., ethyl cellulose? If yes, I couldn't find ethyl group (2:1) mapping parameters, except one in the tutorial that used TP5. Can I use the same, or should I redo parameterization?
Thank you very much for your response
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