Dear colleague,
I am refining a structure containing a carbohydate chain using CNS,
which is SIA(a2-3){Gal(b1-3)GalNac(b1-4)}Gal(b1-4)Glc. I bulit the model of
the carbohydrate chain as five single carbohydrate like residues in peptides.
The parameter and topology files are from CNS. However, CNS consider them as
five molecules but not a chain. My question is how to construct the linkage
between carbohydrates for CNS to refine them as a carbohydrate chain like
residues in peptide. The .pdb file of my carbohydrates is following.
ATOM 1 C1 SIA A 298 -5.799 2.161 -26.738 1.00 34.36 6
ATOM 2 C2 SIA A 298 -5.671 0.671 -26.962 1.00 31.76 6
ATOM 3 C3 SIA A 298 -5.638 0.352 -28.454 1.00 32.16 6
ATOM 4 C4 SIA A 298 -4.364 0.876 -29.124 1.00 31.01 6
ATOM 5 C5 SIA A 298 -3.108 0.412 -28.399 1.00 28.11 6
ATOM 6 C6 SIA A 298 -3.240 0.709 -26.911 1.00 28.56 6
ATOM 7 C7 SIA A 298 -2.064 0.132 -26.117 1.00 26.99 6
ATOM 8 C8 SIA A 298 -2.327 0.184 -24.611 1.00 26.24 6
ATOM 9 C9 SIA A 298 -1.015 0.210 -23.835 1.00 26.43 6
ATOM 10 C10 SIA A 298 -0.814 0.406 -29.304 1.00 28.70 6
ATOM 11 C11 SIA A 298 0.313 1.265 -29.804 1.00 18.45 6
ATOM 12 N5 SIA A 298 -1.915 1.058 -28.920 1.00 31.12 7
ATOM 13 O1A SIA A 298 -6.336 2.867 -27.625 1.00 29.15 8
ATOM 14 O1B SIA A 298 -5.404 2.624 -25.644 1.00 36.52 8
ATOM 15 O4 SIA A 298 -4.324 0.422 -30.484 1.00 31.93 8
ATOM 16 O6 SIA A 298 -4.460 0.160 -26.383 1.00 30.71 8
ATOM 17 O7 SIA A 298 -1.837 -1.222 -26.522 1.00 32.06 8
ATOM 18 O8 SIA A 298 -3.091 1.348 -24.260 1.00 23.18 8
ATOM 19 O9 SIA A 298 -1.281 0.059 -22.435 1.00 25.41 8
ATOM 20 O10 SIA A 298 -0.718 -0.809 -29.255 1.00 32.33 8
ATOM 21 C1 GAL A 299 -6.289 3.311 -20.096 1.00 25.26 6
ATOM 22 C2 GAL A 299 -7.266 4.390 -19.652 1.00 25.78 6
ATOM 23 C3 GAL A 299 -6.509 5.590 -19.087 1.00 25.52 6
ATOM 24 C4 GAL A 299 -5.451 5.166 -18.067 1.00 28.53 6
ATOM 25 C5 GAL A 299 -4.610 4.010 -18.596 1.00 25.75 6
ATOM 26 C6 GAL A 299 -3.682 3.463 -17.519 1.00 27.70 6
ATOM 27 O2 GAL A 299 -8.068 4.799 -20.744 1.00 26.14 8
ATOM 28 O3 GAL A 299 -7.428 6.465 -18.474 1.00 30.49 8
ATOM 29 O4 GAL A 299 -6.068 4.771 -16.860 1.00 29.57 8
ATOM 30 O5 GAL A 299 -5.440 2.962 -19.032 1.00 28.60 8
ATOM 31 O6 GAL A 299 -3.033 2.302 -17.991 1.00 31.34 8
ATOM 32 C1 NGA A 300 -6.337 -0.595 -23.070 1.00 28.11 6
ATOM 33 C2 NGA A 300 -7.066 0.573 -22.405 1.00 26.79 6
ATOM 34 C3 NGA A 300 -6.202 1.254 -21.344 1.00 28.29 6
ATOM 35 C4 NGA A 300 -5.597 0.221 -20.404 1.00 28.03 6
ATOM 36 C5 NGA A 300 -4.892 -0.878 -21.187 1.00 27.92 6
ATOM 37 C6 NGA A 300 -4.337 -1.937 -20.245 1.00 29.15 6
ATOM 38 C7 NGA A 300 -8.738 1.852 -23.615 1.00 26.66 6
ATOM 39 C8 NGA A 300 -8.997 2.884 -24.671 1.00 25.05 6
ATOM 40 N2 NGA A 300 -7.459 1.553 -23.393 1.00 22.87 7
ATOM 41 O3 NGA A 300 -7.020 2.194 -20.631 1.00 27.10 8
ATOM 42 O4 NGA A 300 -6.635 -0.351 -19.605 1.00 34.07 8
ATOM 43 O5 NGA A 300 -5.806 -1.488 -22.096 1.00 27.66 8
ATOM 44 O6 NGA A 300 -3.460 -2.806 -20.972 1.00 31.34 8
ATOM 45 O7 NGA A 300 -9.648 1.324 -23.000 1.00 26.79 8
ATOM 46 C1 GAL A 301 -8.740 -3.102 -26.426 1.00 44.56 6
ATOM 47 C2 GAL A 301 -8.407 -1.636 -26.696 1.00 40.52 6
ATOM 48 C3 GAL A 301 -6.950 -1.312 -26.381 1.00 35.19 6
ATOM 49 C4 GAL A 301 -6.532 -1.910 -25.053 1.00 34.19 6
ATOM 50 C5 GAL A 301 -6.862 -3.393 -25.047 1.00 40.29 6
ATOM 51 C6 GAL A 301 -6.375 -4.085 -23.775 1.00 42.31 6
ATOM 52 O2 GAL A 301 -8.675 -1.358 -28.056 1.00 38.59 8
ATOM 53 O3 GAL A 301 -6.831 0.079 -26.335 1.00 35.06 8
ATOM 54 O4 GAL A 301 -7.210 -1.238 -24.016 1.00 29.27 8
ATOM 55 O5 GAL A 301 -8.263 -3.522 -25.167 1.00 41.33 8
ATOM 56 O6 GAL A 301 -6.752 -5.443 -23.791 1.00 50.74 8
ATOM 57 C2 GLC A 302 -11.902 -6.342 -25.344 1.00 64.49 6
ATOM 58 C3 GLC A 302 -11.437 -4.894 -25.352 1.00 62.01 6
ATOM 59 C4 GLC A 302 -10.468 -4.657 -26.503 1.00 60.61 6
ATOM 60 C5 GLC A 302 -11.080 -5.134 -27.814 1.00 62.56 6
ATOM 61 C6 GLC A 302 -10.096 -4.956 -28.963 1.00 60.98 6
ATOM 62 C1 GLC A 302 -12.402 -6.767 -26.721 1.00 66.71 6
ATOM 63 O1 GLC A 302 -12.661 -8.153 -26.709 1.00 71.09 8
ATOM 64 O2 GLC A 302 -12.939 -6.491 -24.400 1.00 63.57 8
ATOM 65 O3 GLC A 302 -10.807 -4.594 -24.128 1.00 61.51 8
ATOM 66 O4 GLC A 302 -10.159 -3.283 -26.587 1.00 53.36 8
ATOM 67 O5 GLC A 302 -11.434 -6.496 -27.713 1.00 66.33 8
ATOM 68 O6 GLC A 302 -10.580 -3.973 -29.850 1.00 62.54 8
Your sincerely
De-Feng Li
[email protected]
2009-05-27
Defeng Li, Dr.,
Email: [email protected]
National Laboratory of Biomacromolecules,
Institute of Biophysics, Chinese Academy of Sciences,
15 Datun Road, Chaoyang District,
Beijing 100101, China
