Date: Tue, 9 Nov 2021 13:41:21 -0600
Hi Dear Amber users
Sorry if my question sounds very amatuer, as I'm very new to using Amber.
I'm trying to use Glycam06 FF to simulate cellulose crystal where the
surface is functionalized with COOH (H61 and H62 are replaced by oxygen to
form C=O, image attached)
For intact cellulose units I use the following charge parameters based on
the literature:
Carbons:
C1: 0.3840,C2: 0.3100,C3: 0.2840, C4: 0.2760 , C5: 0.2250 , C6: 0.2820
Oxygens:
O1:-0.6390
O2:-0.7180
O3:-0.7090
O4:-0.4680 (Os, linkage), -0.7140 (Oh, end)
O5:-0.4710
O6:-0.6880
Hydrogens:
HO1: 0.4450
HO2: 0.4370
HO3: 0.4320
HO4: 0.4400
HO6: 0.4240
and other Hydrogens are zero charged. The following are my questions:
1 - how are the charges affected by adding O=C6 (O2 sp2 oxygen) to C6 (C
Sp2 carbon) carbon, particularly the charges of C6 and O6 and O=C6? Are
they defined in the Glycam06 framework for carbohydrates or RESP
calculation is required? If not, is it reasonable to apply AM1-BCC method
for only that glucose to adjust the charges?
2- I found the following bonded parameters undefined too by using tleap. Is
it reasonable to use gaff for these parameters and add them to the rest of
Glycam parameters for the cellulose system.
Error: ** No torsion terms for Cg-C-Oh-Ho
Error: ** No torsion terms for H1-Cg-C-Oh
Error: ** No torsion terms for Os-Cg-C-Oh
Error: ** No torsion terms for Cg-Cg-C-Oh
Error: ** No torsion terms for Ho-Oh-C-O2
Error: ** No angle terms for Cg - C - Oh
Error: ** No angle terms for Cg - C - Oh
Error: ** No bond terms for C-Oh
I would appreciate your response and suggestions very very much
Thanks for your helps
Best regards
Arash
[image: image.png]
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