PDB upload problem

HADDOCK
21

thanks. I sent it however is processing. I have another one. This could be a good start point or i have to edit?
prueba.pdf (707.4 KB)

22

For sure the .pdf extension is not appropriate.

23

i did not use pdf i only used that to upload here

24

I need you help.

I tried to upload a pdb with a molecule and a ligand (i exported from pymol) file name: UGT2_UDP_Glc_AF3
UGT2_UDP_Glc_AF3.txt (272.8 KB)
UGT2_UDP_Glc_AF3editada.txt (365.6 KB)
UGT2_UDP_Glc_AF3editadaSinhidrogenos.txt (353.0 KB)
…It did not work.

So as you teached me i tried to rename the ligand: UGT2_UDP_Glc_AF3editada. It neither work :frowning:

So I tried to earease the hydrogen ot the protein: UGT2_UDP_Glc_AF3editadaSinhidrogenos neither worked :frowning:

25

Error during the reading of the mmCIF file UGT2_UDP_Glc_AF3.cif. ‘_atom_site.id’.
it says, could you help me?

26

could you help me?

27

I would advise to:

  • Separate the ligand and the protein in two different files
  • Generate .pdb files instead of .cif (export with PyMol)
  • Change HETATM to ATOM for the ligand
  • Add a chain id to the ligand (using pdb-tools for example)

P.S: also read the AlphaFoldSever terms and conditions on how you can/cannot use their outputs

28

thanks. The problem is that i could not separate because i have two ligands to dock in a protein.

  • Add a chain id to the ligand (using pdb-tools for example)
    how could i perform this?
    P.S: also read the AlphaFoldSever terms and conditions on how you can/cannot use their outputs
    what you mean about this?
29

The problem is that i could not separate because i have two ligands to dock in a protein.

Then simply separate into three different files (and three different chains)

Add a chain id to the ligand (using pdb-tools for example)
how could i perform this?

We provide an online version of pdb-tools here, where you can use the pdb_chains tool to modify the chain id of your ligand.

read the AlphaFoldSever terms and conditions on how you can/cannot use their outputs
what you mean about this?

In the AlphaFoldServer home page you will find this statement:

AlphaFold Server output cannot be used in docking or screening tools

30

I realized that my answer was not accurate:

If you already have a bound ligand that you do not want to move, this ligand must have:

  • the same chain id as your protein
  • be placed in the same file as your protein
  • start with HETATM for all coodinates of that ligand

Regarding the other one, it should be in an other file.