Missing Alpha Carbons

Beril · May 20, 2020, 12:40pm

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 ATOM 1801 CA ARG A 350 ATOM 1802 C ARG A 350 ATOM 1803 O ARG A 350 ATOM 1804 CB ARG A 350 ATOM 1805 CG ARG A 350 ATOM 1806 CD ARG A 350 ATOM 1807 NE ARG A 350 ATOM 1808 CZ ARG A 350 ATOM 1809 NH1 ARG A 350 ATOM 1810 NH2 ARG A 350 ATOM 1811 N ILE A 351 ATOM 1812 CA ILE A 351 ATOM 1813 C ILE A 351 ATOM 1814 O ILE A 351 ATOM 1815 CB ILE A 351 ATOM 1816 CG1 ILE A 351 ATOM 1817 CG2 ILE A 351 ATOM 1818 CD1 ILE A 351 TER
HETATM 1819 N SCN A 15 HETATM 1820 C SCN A 15 HETATM 1821 S SCN A 15 CONECT 1819 1820
CONECT 1820 1819 1821
CONECT 1821 1820
END 20.316 28.436 16.844 1.00 46.08 A N
20.290 29.694 17.589 1.00 47.07 A C
20.987 29.604 18.955 1.00 47.51 A C
20.810 30.476 19.805 1.00 47.68 A O
18.847 30.179 17.736 1.00 47.16 A C
18.322 30.913 16.502 1.00 48.06 A C
16.811 30.815 16.394 1.00 49.42 A C
16.149 31.023 17.681 1.00 49.94 A N
15.612 32.172 18.077 1.00 50.13 A C
15.643 33.235 17.284 1.00 49.91 A N1+
15.036 32.254 19.270 1.00 50.32 A N
21.787 28.550 19.129 1.00 48.18 A N
22.537 28.224 20.362 1.00 48.72 A C
21.684 28.196 21.637 1.00 49.11 A C
20.810 27.335 21.796 1.00 49.39 A O
23.844 29.076 20.546 1.00 48.72 A C
23.530 30.547 20.862 1.00 48.94 A C
24.760 28.927 19.323 1.00 48.70 A C
24.707 31.345 21.428 1.00 50.17 A C
21.587 21.449 7.419 1.00 55.81 C N
20.692 21.588 8.224 1.00 55.66 C C
19.553 22.198 9.459 1.00 55.82 C S

amjjbonvin · May 20, 2020, 6:12pm

Strange - it could be the columns are messed up.

You mentioned you modified the file in PyMol. Did you save it as PDF format from PyMol.

No further edits?

Beril · May 20, 2020, 7:53pm

I have retried from scratch once more. I have used the following commands for the modifications in PyMOL:

fetch 3HK0
remove chain B

I have removed water molecules by Action/Remove waters. I have exported the molecule as .pdb, and tried to submit the same job once more. I am trying to dock Grb10 to a larger molecule that I have used in my previous runs which works fine, so I am using the larger molecule as the first molecule input to the portal, as suggested in a similar post in this forum. Still, I got the following warning:

“The following error occurred when processing one of your PDB file: Could not create unambiguous restraints to keep the bodies together.Please check if your protein is missing alpha-carbons.”

The following are the first and last couples of amino acids from the mentioned PDB file without making any edits:

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 3503 N TYR B 349 15.703 26.503 29.164 1.00 46.69 B N
ATOM 3504 CA TYR B 349 16.241 26.787 30.496 1.00 47.27 B C
ATOM 3505 C TYR B 349 17.774 26.832 30.505 1.00 47.65 B C
ATOM 3506 O TYR B 349 18.370 27.659 31.196 1.00 47.66 B O
ATOM 3507 CB TYR B 349 15.720 25.749 31.499 1.00 47.17 B C
ATOM 3508 CG TYR B 349 16.332 25.828 32.883 1.00 47.42 B C
ATOM 3509 CD1 TYR B 349 17.253 24.869 33.315 1.00 48.17 B C
ATOM 3510 CD2 TYR B 349 15.991 26.854 33.763 1.00 47.45 B C
ATOM 3511 CE1 TYR B 349 17.820 24.931 34.592 1.00 47.79 B C
ATOM 3512 CE2 TYR B 349 16.550 26.927 35.037 1.00 47.46 B C
ATOM 3513 CZ TYR B 349 17.463 25.964 35.443 1.00 47.80 B C
ATOM 3514 OH TYR B 349 18.015 26.037 36.702 1.00 48.15 B O
ATOM 3515 N ARG B 350 18.384 25.938 29.724 1.00 48.26 B N
ATOM 3516 CA ARG B 350 19.843 25.785 29.588 1.00 48.52 B C
ATOM 3517 C ARG B 350 20.530 25.340 30.867 1.00 48.77 B C
ATOM 3518 O ARG B 350 20.734 24.142 31.074 1.00 49.21 B O
ATOM 3519 CB ARG B 350 20.512 27.030 28.982 1.00 48.59 B C
ATOM 3520 CG ARG B 350 20.968 26.817 27.535 1.00 49.15 B C
ATOM 3521 CD ARG B 350 21.290 28.113 26.814 1.00 49.81 B C
ATOM 3522 NE ARG B 350 20.098 28.708 26.213 1.00 50.63 B N
ATOM 3523 CZ ARG B 350 19.428 29.740 26.718 1.00 51.22 B C
ATOM 3524 NH1 ARG B 350 19.825 30.321 27.848 1.00 50.98 B N1+
ATOM 3525 NH2 ARG B 350 18.358 30.200 26.083 1.00 50.94 B N
TER
HETATM 3526 N SCN A 15 21.587 21.449 7.419 1.00 55.81 C N
HETATM 3527 C SCN A 15 20.692 21.588 8.224 1.00 55.66 C C
HETATM 3528 S SCN A 15 19.553 22.198 9.459 1.00 55.82 C S
HETATM 3529 O HOH A 1 20.453 10.971 -7.293 1.00 51.67 D O
HETATM 3530 O HOH A 2 17.066 12.601 -5.383 1.00 47.16 D O
HETATM 3531 O HOH A 3 24.810 -6.133 1.217 1.00 39.02 D O
HETATM 3532 O HOH A 4 4.909 13.309 6.201 1.00 35.87 D O
HETATM 3533 O HOH A 5 9.351 20.106 15.706 1.00 49.38 D O
HETATM 3534 O HOH A 6 14.003 31.461 21.639 1.00 33.52 D O
HETATM 3535 O HOH A 7 22.204 20.032 15.597 1.00 41.79 D O
HETATM 3536 O HOH B 8 -0.474 10.314 22.138 1.00 46.47 E O
HETATM 3537 O HOH B 9 1.174 22.413 25.662 1.00 34.95 E O
HETATM 3538 O HOH B 10 0.760 24.983 29.211 1.00 44.46 E O
HETATM 3539 O HOH B 11 -20.022 22.378 28.856 1.00 49.25 E O
HETATM 3540 O HOH B 12 12.532 27.643 18.450 1.00 44.38 E O
HETATM 3541 O HOH B 13 -4.673 17.696 45.858 1.00 66.97 E O
HETATM 3542 O HOH B 14 -3.883 39.303 19.922 1.00 50.54 E O
CONECT 3526 3527
CONECT 3527 3526 3528
CONECT 3528 3527
END

What do you think? What shall I do?

Thank you so much for the help!

amjjbonvin · May 21, 2020, 7:18am

Hi there

There is something fishy about that PDB file that make PyMol write junk. Also our pdb-tools fail to process it.
If you download instead directly from the PDB a PDB formatted file, things seem to be ok.

https://www.ebi.ac.uk/pdbe/entry-files/pdb3hk0.ent

Beril · May 21, 2020, 8:07am

Thank you so much Professor! It worked!