The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
Hello Everyone,
I am trying to use Grb10 for simulations. I am using 3HK0 model, and I have removed chain B in PyMOL as I am only interested in RA Domain, chain A. When I upload the two molecules to be docked, I receive an error, “Missing Alpha Carbons”. I have checked the model in Notepad, but I couldn’t find out anything suspicious. I am pasting some parts of the document below as well. What do you think that I am doing wrong or incomplete?
Thank you so much for your time!
Best,
Beril
ATOM 1 N LYS A 109 29.154 9.610 35.781 1.00 53.14 A N
ATOM 2 CA LYS A 109 30.454 8.894 35.955 1.00 53.19 A C
ATOM 3 C LYS A 109 30.646 7.812 34.888 1.00 53.28 A C
ATOM 4 O LYS A 109 30.216 6.670 35.065 1.00 53.31 A O
ATOM 5 CB LYS A 109 30.548 8.292 37.360 1.00 53.17 A C
ATOM 6 N GLN A 110 31.288 8.187 33.780 1.00 53.36 A N
ATOM 7 CA GLN A 110 31.541 7.280 32.650 1.00 53.42 A C
ATOM 8 C GLN A 110 32.700 7.749 31.774 1.00 53.31 A C
ATOM 9 O GLN A 110 32.805 8.931 31.448 1.00 53.35 A O
ATOM 10 CB GLN A 110 30.295 7.136 31.770 1.00 53.52 A C
ATOM 11 CG GLN A 110 29.534 5.829 31.932 1.00 53.88 A C
ATOM 12 CD GLN A 110 28.575 5.574 30.778 1.00 54.24 A C
ATOM 13 NE2 GLN A 110 27.279 5.577 31.073 1.00 54.62 A N
ATOM 14 OE1 GLN A 110 28.995 5.375 29.636 1.00 54.13 A O
…
ATOM 1800 N ARG A 350 20.316 28.436 16.844 1.00 46.08 A N
ATOM 1801 CA ARG A 350 20.290 29.694 17.589 1.00 47.07 A C
ATOM 1802 C ARG A 350 20.987 29.604 18.955 1.00 47.51 A C
ATOM 1803 O ARG A 350 20.810 30.476 19.805 1.00 47.68 A O
ATOM 1804 CB ARG A 350 18.847 30.179 17.736 1.00 47.16 A C
ATOM 1805 CG ARG A 350 18.322 30.913 16.502 1.00 48.06 A C
ATOM 1806 CD ARG A 350 16.811 30.815 16.394 1.00 49.42 A C
ATOM 1807 NE ARG A 350 16.149 31.023 17.681 1.00 49.94 A N
ATOM 1808 CZ ARG A 350 15.612 32.172 18.077 1.00 50.13 A C
ATOM 1809 NH1 ARG A 350 15.643 33.235 17.284 1.00 49.91 A N1+
ATOM 1810 NH2 ARG A 350 15.036 32.254 19.270 1.00 50.32 A N
ATOM 1811 N ILE A 351 21.787 28.550 19.129 1.00 48.18 A N
ATOM 1812 CA ILE A 351 22.537 28.224 20.362 1.00 48.72 A C
ATOM 1813 C ILE A 351 21.684 28.196 21.637 1.00 49.11 A C
ATOM 1814 O ILE A 351 20.810 27.335 21.796 1.00 49.39 A O
ATOM 1815 CB ILE A 351 23.844 29.076 20.546 1.00 48.72 A C
ATOM 1816 CG1 ILE A 351 23.530 30.547 20.862 1.00 48.94 A C
ATOM 1817 CG2 ILE A 351 24.760 28.927 19.323 1.00 48.70 A C
ATOM 1818 CD1 ILE A 351 24.707 31.345 21.428 1.00 50.17 A C
TER
HETATM 1819 N SCN A 15 21.587 21.449 7.419 1.00 55.81 C N
HETATM 1820 C SCN A 15 20.692 21.588 8.224 1.00 55.66 C C
HETATM 1821 S SCN A 15 19.553 22.198 9.459 1.00 55.82 C S
CONECT 1819 1820
CONECT 1820 1819 1821
CONECT 1821 1820
END