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GLYCAM-L  May 2019

GLYCAM-L May 2019

Subject:

Non terminal β-D-Glucosamine

From:

Monia Kam <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Fri, 3 May 2019 12:50:17 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (62 lines)

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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