Dear HADDOCK users
I have a problem with the PDB file of the protein starting structure. I have used this pdb file for the haddock server( 2.4) 6 months ago, and I got very good docking results. Now I (guru user) am trying to use the same starting structure again for protein-protein docking on HADDOCK server.
But today I got the error below using the same starting structure…
The following error occurred when processing one of your PDB file: Instances of ligand ASP do not contain the same atoms
ASP is the 1st residue in my protein. Could you give me some suggestions on this problem? Thank you very much1
Thanks
The fact that the message states ligand ASP seems to point to two possible issues:
-
It is defined as HETATM instead of ATOM
-
You wrongly selected ligand as molecule type
Thank you, Dr. Bonvin.
- I checked the pdb file of the starting structure. All the amino acid are defined as ATOM and GDP is defined as HETATM. And when I deleted the first residue ASP, I got the error below
The following error occurred when processing one of your PDB file: Instances of ligand GLY do not contain the same atoms
- For the “What kind of molecule are you docking”
I chose “Protein or Protein-Ligand”
In addition to the two issues you mentioned, are there any other possible reasons that cause my problem?
Thanks,
Stellalink
Can you share this PDB file with us?
Does it contain a single model or an end ensemble?
Hi Bonvin
Sorry for the late reply.
Yes, I am happy to share my PDB file. The structure of interest is a dimer. I submitted this PDB file to HADDOCK2.4 a few months ago, and I got good docking structures for my protein-protein complex. Also, the docking results look good when I submitted this PDB file to Haddock 2.2 server two days ago.
I am new user and I cannot upload the attachment. For the PDB file, please see below. Residues from 10-316 are the 1st molecule, and residues from 1010-1316 are the 2nd molecule. Please let me know if you need more detailed information.
ATOM 1 N ASP 10 93.638 79.298 53.852 1.00 0.00 N
ATOM 2 CA ASP 10 94.118 80.388 54.762 1.00 0.00 C
ATOM 3 C ASP 10 95.608 80.458 55.022 1.00 0.00 C
ATOM 4 O ASP 10 96.198 79.418 55.362 1.00 0.00 O
ATOM 5 CB ASP 10 93.338 80.388 56.082 1.00 0.00 C
ATOM 6 CG ASP 10 91.828 80.518 55.942 1.00 0.00 C
ATOM 7 OD1 ASP 10 91.448 80.608 54.792 1.00 0.00 O
ATOM 8 OD2 ASP 10 91.078 80.588 56.972 1.00 0.00 O1-
ATOM 9 HA ASP 10 93.928 81.308 54.232 1.00 0.00 H
ATOM 10 HB1 ASP 10 93.458 79.408 56.592 1.00 0.00 H
ATOM 11 HB2 ASP 10 93.708 81.228 56.702 1.00 0.00 H
ATOM 12 H1 ASP 10 94.138 79.428 52.952 1.00 0.00 H
ATOM 13 H2 ASP 10 93.838 78.338 54.212 1.00 0.00 H
ATOM 14 H3 ASP 10 92.608 79.298 53.692 1.00 0.00 H
…
ATOM 4433 N GLY 316 118.608 102.648 53.342 1.00 0.00 N
ATOM 4434 CA GLY 316 119.988 102.568 53.752 1.00 0.00 C
ATOM 4435 C GLY 316 120.808 103.408 52.792 1.00 0.00 C
ATOM 4436 OT1 GLY 316 120.298 104.228 52.072 1.00 0.00 O
ATOM 4437 OT2 GLY 316 122.088 103.348 52.942 1.00 0.00 O
ATOM 4438 HN GLY 316 118.488 103.508 52.852 1.00 0.00 H
ATOM 4439 HA1 GLY 316 120.108 103.028 54.722 1.00 0.00 H
ATOM 4440 HA2 GLY 316 120.298 101.538 53.662 1.00 0.00 H
ATOM 4441 N ASP 1010 72.948 85.228 12.572 1.00 0.00 N
ATOM 4442 CA ASP 1010 73.548 85.978 13.742 1.00 0.00 C
ATOM 4443 C ASP 1010 74.938 85.518 14.172 1.00 0.00 C
ATOM 4444 O ASP 1010 75.268 84.348 14.062 1.00 0.00 O
ATOM 4445 CB ASP 1010 72.538 85.968 14.982 1.00 0.00 C
ATOM 4446 CG ASP 1010 71.238 86.748 14.702 1.00 0.00 C
ATOM 4447 OD1 ASP 1010 71.038 87.188 13.582 1.00 0.00 O
ATOM 4448 OD2 ASP 1010 70.418 86.988 15.582 1.00 0.00 O1-
ATOM 4449 HA ASP 1010 73.698 87.028 13.522 1.00 0.00 H
ATOM 4450 HB1 ASP 1010 72.218 84.978 15.382 1.00 0.00 H
ATOM 4451 HB2 ASP 1010 73.048 86.468 15.832 1.00 0.00 H
ATOM 4452 H1 ASP 1010 72.528 84.348 12.902 1.00 0.00 H
ATOM 4453 H2 ASP 1010 72.238 85.728 12.012 1.00 0.00 H
ATOM 4454 H3 ASP 1010 73.788 84.908 12.042 1.00 0.00 H
…
ATOM 8873 N GLY 1316 103.028 101.528 11.292 1.00 0.00 N
ATOM 8874 CA GLY 1316 104.348 101.038 11.512 1.00 0.00 C
ATOM 8875 C GLY 1316 105.388 102.198 11.582 1.00 0.00 C
ATOM 8876 OT1 GLY 1316 105.058 103.378 11.672 1.00 0.00 O
ATOM 8877 OT2 GLY 1316 106.558 101.758 11.852 1.00 0.00 O
ATOM 8878 HN GLY 1316 102.978 102.498 11.072 1.00 0.00 H
ATOM 8879 HA1 GLY 1316 104.408 100.498 12.442 1.00 0.00 H
ATOM 8880 HA2 GLY 1316 104.648 100.398 10.692 1.00 0.00 H
TER
HETATM 8881 PA GDP 1317 113.158 93.498 79.502 1.00 0.00 P
HETATM 8882 PB GDP 1317 113.648 90.918 78.782 1.00 0.00 P
HETATM 8883 C5’ GDP 1317 113.788 95.178 77.542 1.00 0.00 C
HETATM 8884 O5’ GDP 1317 112.988 94.828 78.732 1.00 0.00 O
HETATM 8885 C4’ GDP 1317 113.358 96.388 76.672 1.00 0.00 C
HETATM 8886 O4’ GDP 1317 111.938 96.548 76.492 1.00 0.00 O
HETATM 8887 C3’ GDP 1317 113.758 97.818 77.192 1.00 0.00 C
HETATM 8888 O3’ GDP 1317 114.918 97.858 78.022 1.00 0.00 O
HETATM 8889 C2’ GDP 1317 112.558 98.318 77.932 1.00 0.00 C
HETATM 8890 O2’ GDP 1317 112.498 99.738 77.932 1.00 0.00 O
HETATM 8891 C1’ GDP 1317 111.468 97.658 77.222 1.00 0.00 C
HETATM 8892 N1 GDP 1317 106.488 97.088 78.082 1.00 0.00 N
HETATM 8893 O1A GDP 1317 111.978 93.268 80.392 1.00 0.00 O1-
HETATM 8894 O1B GDP 1317 113.978 90.378 77.402 1.00 0.00 O
HETATM 8895 C2 GDP 1317 107.148 97.428 76.852 1.00 0.00 C
HETATM 8896 N2 GDP 1317 106.358 97.648 75.752 1.00 0.00 N
HETATM 8897 O2A GDP 1317 114.428 93.628 80.302 1.00 0.00 O
HETATM 8898 O2B GDP 1317 114.888 90.868 79.702 1.00 0.00 O1-
HETATM 8899 N3 GDP 1317 108.478 97.548 76.782 1.00 0.00 N
HETATM 8900 O3A GDP 1317 113.328 92.418 78.452 1.00 0.00 O
HETATM 8901 O3B GDP 1317 112.478 90.248 79.402 1.00 0.00 O
HETATM 8902 C4 GDP 1317 109.078 97.378 77.942 1.00 0.00 C
HETATM 8903 C5 GDP 1317 108.488 97.008 79.142 1.00 0.00 C
HETATM 8904 C6 GDP 1317 107.118 96.918 79.262 1.00 0.00 C
HETATM 8905 O6 GDP 1317 106.518 96.568 80.292 1.00 0.00 O
HETATM 8906 N7 GDP 1317 109.408 96.888 80.132 1.00 0.00 N
HETATM 8907 C8 GDP 1317 110.518 97.108 79.522 1.00 0.00 C
HETATM 8908 N9 GDP 1317 110.418 97.398 78.142 1.00 0.00 N
HETATM 8909 PA GDP 1318 97.948 92.658 38.362 1.00 0.00 P
HETATM 8910 PB GDP 1318 97.628 90.258 37.152 1.00 0.00 P
HETATM 8911 C5’ GDP 1318 98.408 94.168 36.342 1.00 0.00 C
HETATM 8912 O5’ GDP 1318 97.858 94.078 37.732 1.00 0.00 O
HETATM 8913 C4’ GDP 1318 97.958 95.438 35.422 1.00 0.00 C
HETATM 8914 O4’ GDP 1318 96.488 95.468 35.542 1.00 0.00 O
HETATM 8915 C3’ GDP 1318 98.518 96.868 35.652 1.00 0.00 C
HETATM 8916 O3’ GDP 1318 98.898 97.168 36.942 1.00 0.00 O
HETATM 8917 C2’ GDP 1318 97.358 97.658 35.212 1.00 0.00 C
HETATM 8918 O2’ GDP 1318 97.468 98.108 33.892 1.00 0.00 O
HETATM 8919 C1’ GDP 1318 96.138 96.858 35.342 1.00 0.00 C
HETATM 8920 N1 GDP 1318 91.498 98.488 36.702 1.00 0.00 N
HETATM 8921 O1A GDP 1318 96.748 92.418 39.202 1.00 0.00 O1-
HETATM 8922 O1B GDP 1318 98.118 89.858 35.742 1.00 0.00 O
HETATM 8923 C2 GDP 1318 92.028 98.458 35.402 1.00 0.00 C
HETATM 8924 N2 GDP 1318 91.158 98.748 34.402 1.00 0.00 N
HETATM 8925 O2A GDP 1318 99.248 92.758 39.122 1.00 0.00 O
HETATM 8926 O2B GDP 1318 98.358 89.428 38.162 1.00 0.00 O1-
HETATM 8927 N3 GDP 1318 93.248 97.938 35.162 1.00 0.00 N
HETATM 8928 O3A GDP 1318 98.128 91.728 37.202 1.00 0.00 O
HETATM 8929 O3B GDP 1318 96.108 90.198 37.292 1.00 0.00 O
HETATM 8930 C4 GDP 1318 93.948 97.728 36.272 1.00 0.00 C
HETATM 8931 C5 GDP 1318 93.588 97.978 37.612 1.00 0.00 C
HETATM 8932 C6 GDP 1318 92.248 98.298 37.862 1.00 0.00 C
HETATM 8933 O6 GDP 1318 91.708 98.298 38.942 1.00 0.00 O
HETATM 8934 N7 GDP 1318 94.608 97.848 38.472 1.00 0.00 N
HETATM 8935 C8 GDP 1318 95.618 97.478 37.712 1.00 0.00 C
HETATM 8936 N9 GDP 1318 95.268 97.268 36.432 1.00 0.00 N
CONECT 8881 8893 8897 8900 8884
CONECT 8882 8894 8898 8901 8900
CONECT 8883 8884 8885
CONECT 8884 8883 8881
CONECT 8885 8883 8886 8887
CONECT 8886 8885 8891
CONECT 8887 8885 8888 8889
CONECT 8888 8887
CONECT 8889 8887 8890 8891
CONECT 8890 8889
CONECT 8891 8886 8889 8908
CONECT 8892 8904 8895
CONECT 8893 8881
CONECT 8894 8882
CONECT 8895 8892 8896 8899
CONECT 8896 8895
CONECT 8897 8881
CONECT 8898 8882
CONECT 8899 8895 8902
CONECT 8900 8881 8882
CONECT 8901 8882
CONECT 8902 8899 8903 8908
CONECT 8903 8902 8906 8904
CONECT 8904 8892 8903 8905
CONECT 8905 8904
CONECT 8906 8903 8907
CONECT 8907 8906 8908
CONECT 8908 8891 8902 8907
CONECT 8909 8921 8925 8928 8912
CONECT 8910 8922 8926 8929 8928
CONECT 8911 8912 8913
CONECT 8912 8911 8909
CONECT 8913 8911 8914 8915
CONECT 8914 8913 8919
CONECT 8915 8913 8916 8917
CONECT 8916 8915
CONECT 8917 8915 8918 8919
CONECT 8918 8917
CONECT 8919 8914 8917 8936
CONECT 8920 8932 8923
CONECT 8921 8909
CONECT 8922 8910
CONECT 8923 8920 8924 8927
CONECT 8924 8923
CONECT 8925 8909
CONECT 8926 8910
CONECT 8927 8923 8930
CONECT 8928 8909 8910
CONECT 8929 8910
CONECT 8930 8927 8931 8936
CONECT 8931 8930 8934 8932
CONECT 8932 8920 8931 8933
CONECT 8933 8932
CONECT 8934 8931 8935
CONECT 8935 8934 8936
CONECT 8936 8919 8930 8935
END
Thank you very much,
Stellalink
Email otherwise the file to haddock.support@gmail.com
What are the differences between HADDOCK2.2 and HADDOCK2.4.
I am a guru user and I use my experimental distance restraints for protein-protein docking. I know my PDB file has no problems for HADDOCK2.2. If no big differences, I can use HADDOCK2.2.
Thanks,
Xu
2.2 will be discontinued in the future
Thank you, Dr. Bonvin. I just emailed PDB file to haddock.support@gmail.com.
Stellalink