Missing OXT atom after Protein-Ligand Docking

HADDOCK
1

Hi all, I’m using the HADDOCK2.4 webserver to perform a Protein-Ligand Docking.
My ligand is a L-Asp residue generate by the PRODRG web server in a pdb format.
Somehow my OXT atom is missing the HADDOCK results. I’ve tried every solution in this topic: The missing atoms on my ligand - #5 by WayneLaw

I’ve made some attempts with:

Ligand coordinates below and selected Ligand in my Partner 2:

ATOM 1 O ASP A 1 5.128 -4.014 30.331 1.00 0.00 O
ATOM 2 C ASP A 1 5.413 -2.999 30.994 1.00 0.00 C
ATOM 3 OXT ASP A 1 5.229 -1.821 30.619 1.00 0.00 O
ATOM 4 CA ASP A 1 6.126 -3.249 32.308 1.00 0.00 C
ATOM 5 HA ASP A 1 5.387 -3.387 33.098 1.00 0.00 H
ATOM 6 N ASP A 1 6.814 -4.503 32.041 1.00 0.00 N
ATOM 7 H2 ASP A 1 6.149 -5.206 31.817 1.00 0.00 H
ATOM 8 H3 ASP A 1 7.317 -4.777 32.871 1.00 0.00 H
ATOM 9 H1 ASP A 1 7.453 -4.385 31.290 1.00 0.00 H
ATOM 10 CB ASP A 1 7.083 -2.128 32.708 1.00 0.00 C
ATOM 11 HB1 ASP A 1 6.519 -1.250 33.022 1.00 0.00 H
ATOM 12 HB2 ASP A 1 7.755 -1.960 31.866 1.00 0.00 H
ATOM 13 CG ASP A 1 7.929 -2.649 33.868 1.00 0.00 C
ATOM 14 OD2 ASP A 1 7.268 -3.097 34.830 1.00 0.00 O
ATOM 15 OD1 ASP A 1 9.051 -3.082 33.547 1.00 0.00 O
CONECT 2 4 1 3
CONECT 4 10 6 2 5
CONECT 10 11 4 13 12
CONECT 13 10 14 15
CONECT 9 6
CONECT 7 6
CONECT 8 6
CONECT 5 4
CONECT 11 10
CONECT 12 10
CONECT 6 8 7 4 9
CONECT 1 2
CONECT 15 13
CONECT 14 13
CONECT 3 2
END

Ligand coordinates below and selected Ligand in my Partner 2 (In this, the OXT exists but the CA atom is replaced by a Calcium Ion, just as in the previous topic):

HETATM 1 N LIG A 401 78.034 17.068 33.263 1.00 25.39 N
HETATM 2 CA LIG A 401 77.251 16.251 34.155 1.00 23.54 C
HETATM 3 C LIG A 401 77.327 14.829 33.600 1.00 23.27 C
HETATM 4 O LIG A 401 76.592 14.555 32.643 1.00 18.48 O
HETATM 5 CB LIG A 401 75.815 16.778 34.248 1.00 27.01 C
HETATM 6 CG LIG A 401 74.839 15.921 35.059 1.00 26.68 C
HETATM 7 OD1 LIG A 401 73.715 16.446 35.344 1.00 23.44 O
HETATM 8 OD2 LIG A 401 75.208 14.733 35.394 1.00 22.41 O
HETATM 9 OXT LIG A 401 78.139 14.018 34.122 1.00 21.91 O
HETATM 10 HA LIG A 401 77.703 16.271 35.147 1.00 0.00 H
HETATM 11 HB2 LIG A 401 75.424 16.861 33.234 1.00 0.00 H
HETATM 12 HB3 LIG A 401 75.843 17.775 34.688 1.00 0.00 H
HETATM 13 H1 LIG A 401 78.020 18.026 33.583 1.00 0.00 H
HETATM 14 H2 LIG A 401 78.987 16.733 33.248 1.00 0.00 H
HETATM 15 H3 LIG A 401 77.645 17.018 32.332 1.00 0.00 H
CONECT 3 9 2 4
CONECT 2 3 5 10 1
CONECT 5 2 12 6 11
CONECT 6 8 7 5
CONECT 13 1
CONECT 14 1
CONECT 15 1
CONECT 10 2
CONECT 11 5
CONECT 12 5
CONECT 1 14 2 13 15
CONECT 4 3
CONECT 7 6
CONECT 8 6
CONECT 9 3
END

Ligand coordinates below and selected Protein in my Partner 2:

ATOM 1 O ASP A 1 5.128 -4.014 30.330 1.00 0.00 O
ATOM 2 C ASP A 1 5.413 -2.999 30.994 1.00 0.00 C
ATOM 3 OXT ASP A 1 5.229 -1.821 30.619 1.00 0.00 O
ATOM 4 CA ASP A 1 6.126 -3.249 32.308 1.00 0.00 C
ATOM 5 HA ASP A 1 5.387 -3.387 33.098 1.00 0.00 H
ATOM 6 N ASP A 1 6.813 -4.503 32.041 1.00 0.00 N
ATOM 7 H2 ASP A 1 6.149 -5.206 31.817 1.00 0.00 H
ATOM 8 H3 ASP A 1 7.317 -4.777 32.871 1.00 0.00 H
ATOM 9 H1 ASP A 1 7.453 -4.385 31.290 1.00 0.00 H
ATOM 10 CB ASP A 1 7.083 -2.128 32.708 1.00 0.00 C
ATOM 11 HB1 ASP A 1 6.519 -1.250 33.022 1.00 0.00 H
ATOM 12 HB2 ASP A 1 7.755 -1.960 31.866 1.00 0.00 H
ATOM 13 CG ASP A 1 7.929 -2.649 33.868 1.00 0.00 C
ATOM 14 OD2 ASP A 1 7.268 -3.097 34.830 1.00 0.00 O
ATOM 15 OD1 ASP A 1 9.051 -3.082 33.547 1.00 0.00 O
CONECT 2 4 3 1
CONECT 4 2 6 5 10
CONECT 10 4 12 11 13
CONECT 13 15 14 10
CONECT 9 6
CONECT 7 6
CONECT 8 6
CONECT 5 4
CONECT 11 10
CONECT 12 10
CONECT 6 4 8 9 7
CONECT 1 2
CONECT 15 13
CONECT 14 13
CONECT 3 2
END

Is there anything I can try? I’ve also read the HADDOCK Manual but not found the solution.

Thanks in advance,
All the best!

2

By default termini are uncharged (often because the PDB might not represent the full sequence that we used in the experiments).
Provided you have expert/guru access you can specific the termini state of each molecule in the first submission tab.

3

I see, thanks for the answer!
I have the EASY access only.
And may I ask, what are the right way to perform my analysis? With the atoms named as HETATM or ATOM, residue named as ASP or LIG and in with which format, as Ligand or Protein?

4

If you are only docking an ASP, then simply as ATOM and as Protein

5

Thank you very much!