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Date: | Fri, 3 May 2019 12:50:17 -0400 |
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Hello Glycam users,
I'm trying to build a model for a Chitosan dimer using all the possibilities ( Deacetylated and acetylated units) as well as protonated NH3+ and deprotonated NH2 units, I've managed to build the ones where the β-D-Glucosamine and the protonated β-D-Glucosamine are terminals, and I have also found in this mailing list a prep file provided by Arunima for the non-terminal protonated version, whereas I also need a non-terminal β-D-Glucosamine connected by means of β 1 -> 4 linkages.
Another question sinsce I'm a beginner with Amber I'm trying to figure out what all the columns means in the prep file, I've understood the first 4 and the last but what about the columns 5 to 10? I'm having a hard time finding the information
Alpha-D-Glucosamine
0YN INT 0
CORRECT OMIT DU BEG
0.1940
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.0000
2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.0000
3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.0000
4 C1 Cg M 3 2 1 1.388 115.295 -64.277 0.3450
5 H1 H2 E 4 3 2 1.084 109.999 -49.072 0.0000
6 O5 Os E 4 3 2 1.391 112.070 67.910 -0.4770
7 C2 Cg M 4 3 2 1.528 107.801 -169.411 0.4170
8 H2 H1 E 7 4 3 1.084 107.322 174.829 0.0000
9 N2 N B 7 4 3 1.432 112.715 56.414 -1.0240
10 H2A H E 9 7 4 0.991 120.269 -61.776 0.3720
11 H2B H E 9 7 4 0.991 120.544 118.149 0.3720
12 C3 Cg M 7 4 3 1.529 109.215 -69.355 0.1840
13 H3 H1 E 12 7 4 1.088 109.295 65.468 0.0000
14 O3 Oh S 12 7 4 1.404 111.312 -173.132 -0.7000
15 H3O Ho E 14 12 7 0.949 107.869 -52.581 0.4150
16 C4 Cg M 12 7 4 1.517 110.451 -54.088 0.3340
17 H4 H1 E 16 12 7 1.084 108.735 -64.461 0.0000
18 O4 Oh S 16 12 7 1.402 111.001 173.727 -0.7160
19 H4O Ho E 18 16 12 0.949 107.913 54.469 0.4450
20 C5 Cg M 16 12 7 1.526 109.883 54.679 0.2430
21 H5 H1 E 20 16 12 1.086 108.317 66.247 0.0000
22 C6 Cg M 20 16 12 1.515 113.127 -174.629 0.2520
23 H6A H E 22 20 16 1.086 108.283 177.684 0.0000
24 H6B H1 E 22 20 16 1.08 108.199 -64.694 0.0000
25 O6 Oh M 22 20 16 1.402 109.685 56.655 -0.7120
26 H6O Ho E 25 22 20 0.946 109.383 -173.213 0.4440
LOOP
C5 O5
IMPROPER
C2 N2 H2A H2B
DONE
Thank you
Best wishes,
K.Monia
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