# PDB-ERROR: Missing residues **URL:** \ **Category:** Uncategorized\ **Created:** [January 22, 2025, 7:15pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399 "2025-01-22T19:15:50Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [January 22, 2025, 7:15pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/1 "2025-01-22T19:15:50Z")
Hello, Unfortunately, it won’t let me add a photo here. But with some PDBs (unedited from PDB website) that I add onto the Haddock2.4 website, there are multiple errors. The first being that on the next page where I have to select active residues, only some appear. So it looks something like this: R\_ \_ _SPI_ \_ \_ \_ \_ I am not sure what causes this. Any help would be much appreciated. Thanks ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [January 23, 2025, 7:50am UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/2 "2025-01-23T07:50:19Z")
Check your PDB file. There might be modified residues at those positions, not supported by HADDOCK And never a good idea to use PDB files directly from the PDB site without checking what is inside those and removing any unneeded “junk” ---
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [January 23, 2025, 4:01pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/3 "2025-01-23T16:01:48Z")
Usually I remove some of the ‘junk’ via ChimeraX. Such as removing water molecules or other non standard residues. Is there an alternative method? Or sometimes it comes up with: Error in PDB file. Your PDB contains multiple residues with number 60 in chain A or duplicated atom names. How can I rectify this? Thank you ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [January 24, 2025, 2:12pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/4 "2025-01-24T14:12:52Z")
> Usually I remove some of the ‘junk’ via ChimeraX. Such as removing water molecules or other non standard residues. Is there an alternative method? It’s fine as long as your remove the “junk” 🙂 > Or sometimes it comes up with: Error in PDB file. Your PDB contains multiple residues with number 60 in chain A or duplicated atom names. This happens with high resolution crystal structures that might have multiple conformations of some side-chains. You will have to select one per side-chain. Our pdb-tools pdb\_selaltloc can do that ---
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [January 24, 2025, 5:21pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/5 "2025-01-24T17:21:57Z")
Thank you, I did this then went to add the pdb again but when I submit that tab it comes up with: Error in PDB file. Unknown error: list index out of range How can this be rectified? Thank you ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [January 25, 2025, 6:51pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/6 "2025-01-25T18:51:29Z")
Did you use our pdb-tools to correct the PDB file? ---
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [January 27, 2025, 6:22pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/7 "2025-01-27T18:22:27Z")
Unfortunately not. After using the pdb tool and trying to put it in the docking again it comes up with this message: Error in PDB file. Unknown error: list index out of range ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [January 27, 2025, 7:09pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/8 "2025-01-27T19:09:16Z")
Try adding a pdb\_tidy final step when preparing your PDB file And/or share your PDB file ---
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [February 19, 2025, 11:13pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/9 "2025-02-19T23:13:29Z")
Hi, I edit my peptide from a known pdb, using chimeraX. On there I can see that my peptide is cyclic and the disulfide bond present. After using the online Haddock2.4, I download the pdb of the top complex. When I observe it in chimeraX, I notice that the cyclic peptide no longer looks bound together and neither is the disulfide bond. Do you know what causes this and how I can change that? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [February 20, 2025, 10:10am UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/10 "2025-02-20T10:10:09Z")
Did you specify on the server that the peptide should be cyclic? Do you have a run number for this one? ---
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [February 20, 2025, 5:58pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/11 "2025-02-20T17:58:09Z")
Yes I did specify cyclic peptide. This is the link to it as I am not sure on the run number [https://rascar.science.uu.nl/haddock2.4/result/9938322197/446453-HEPSIN-SFTI-V8-TRIAD](https://rascar.science.uu.nl/haddock2.4/result/9938322197/446453-HEPSIN-SFTI-V8-TRIAD) The break in the cyclic peptide is always between amino acid 1 and 14 ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [February 20, 2025, 6:51pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/12 "2025-02-20T18:51:58Z")
The peptide is cyclic! It is a visualisation artefact 🙂 switch to a sticks representation instead of ribbon and you will see it is cyclic. ---
**Author:** ![Sabrina](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Post date:** [February 20, 2025, 7:26pm UTC](https://ask.bioexcel.eu/t/pdb-error-missing-residues/5399/13 "2025-02-20T19:26:36Z")
In stick representation I also see the bond break but maybe that is just an issue with ChimeraX. Thank you for checking though, I just wanted to be sure that my haddock scores were accurate