# PDB upload problem **URL:** \ **Category:** HADDOCK\ **Created:** [February 4, 2022, 11:36pm UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445 "2022-02-04T23:36:14Z")\ **Posts on this page:** 10\ **Page:** 2
**Author:** ![clarisa](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@clarisa](https://ask.bioexcel.eu/u/clarisa)\ **Post date:** [June 13, 2024, 9:14am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/21 "2024-06-13T09:14:14Z")
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](https://ask.bioexcel.eu/uploads/short-url/50ZslB1gaCxaKItfzGOHGT8uEWm.pdf) (707.4 KB) ---
**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Post date:** [June 13, 2024, 9:58am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/22 "2024-06-13T09:58:46Z")
For sure the `.pdf` extension is not appropriate. ---
**Author:** ![clarisa](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@clarisa](https://ask.bioexcel.eu/u/clarisa)\ **Post date:** [June 13, 2024, 10:03am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/23 "2024-06-13T10:03:21Z")
i did not use pdf i only used that to upload here ---
**Author:** ![clarisa](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@clarisa](https://ask.bioexcel.eu/u/clarisa)\ **Post date:** [June 13, 2024, 10:08am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/24 "2024-06-13T10:08:47Z")
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](https://ask.bioexcel.eu/uploads/short-url/2hKiCbUcgRxGvyWpRZ9udhYGaHJ.txt) (272.8 KB) [UGT2\_UDP\_Glc\_AF3editada.txt](https://ask.bioexcel.eu/uploads/short-url/Ar5hDJK458X6FPE9XUarOXOGJpd.txt) (365.6 KB) [UGT2\_UDP\_Glc\_AF3editadaSinhidrogenos.txt](https://ask.bioexcel.eu/uploads/short-url/8qHbRGfDPnfrc5ijm7FApFJl5wf.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 ☹ So I tried to earease the hydrogen ot the protein: UGT2\_UDP\_Glc\_AF3editadaSinhidrogenos neither worked ☹ ---
**Author:** ![clarisa](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@clarisa](https://ask.bioexcel.eu/u/clarisa)\ **Post date:** [June 13, 2024, 10:10am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/25 "2024-06-13T10:10:00Z")
Error during the reading of the mmCIF file UGT2\_UDP\_Glc\_AF3.cif. ‘\_atom\_site.id’. it says, could you help me? ---
**Author:** ![clarisa](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@clarisa](https://ask.bioexcel.eu/u/clarisa)\ **Post date:** [June 13, 2024, 10:10am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/26 "2024-06-13T10:10:14Z")
could you help me? ---
**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Post date:** [June 13, 2024, 10:23am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/27 "2024-06-13T10:23:10Z")
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 ---
**Author:** ![clarisa](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@clarisa](https://ask.bioexcel.eu/u/clarisa)\ **Post date:** [June 15, 2024, 10:43am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/28 "2024-06-15T10:43:43Z")
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? ---
**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Post date:** [June 18, 2024, 9:14am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/29 "2024-06-18T09:14:10Z")
> 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](https://rascar.science.uu.nl/pdbtools/), 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](https://alphafoldserver.com/about) home page you will find this statement: `AlphaFold Server output cannot be used in docking or screening tools` ---
**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Post date:** [June 18, 2024, 10:04am UTC](https://ask.bioexcel.eu/t/pdb-upload-problem/3445/30 "2024-06-18T10:04:38Z")
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. [Previous page](https://ask.bioexcel.eu/t/pdb-upload-problem/3445.md?page=1)