# Haddock: error uploding a PDB file with metals **URL:** \ **Category:** HADDOCK\ **Created:** [May 17, 2024, 12:16pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016 "2024-05-17T12:16:58Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)\ **Post date:** [May 17, 2024, 12:16pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/1 "2024-05-17T12:16:58Z")
Hello Dr. Bonvin and All, I’m having some problems regarding the docking between two proteins tin order to make a homodimer. Both of proteins are in their holo state, with a Zn ion and a Cu one. At first, when I tried to upload them into Haddock, it returned me the following error: “Error in PDB file. Issue when parsing the PDB file at line **1139**. Your PDB contains an elemental ion **ZN without specified charge** ” In order to solve it, I changed the PDB following the guidelines at the following link: [HADDOCK Web Server - Settings](https://wenmr.science.uu.nl/haddock2.4/library) In particular, I wrote ZN+2 instead of ZN for the atom and ZN2 instead of ZN for the residue. When I uploaded the new PDBs into haddock, it returned me the following error: “Error in PDB file. Issue when parsing the PDB file at line **1139**. Your PDB contains multiple forms of the same residue **ZN2 201**. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble.” After that error, I read a bit on the forum and I tried to use the web pdbtools, uploading the structure and running the code just using the main: “pdb\_selaltloc”, without pre-processing or post-processing operations. So I uploaded the third new PDB file, the one from pdbtools, into Haddock, and it returned me the following error: “Error in PDB file. Unknown error: invalid literal for int() with base 10: '+ '” I searched this last error on the forum and I didn’t came up with a solution yet. In the following image, there are the last parts of the PDB files used when I encountered these errors: - The original one; - The corrected one with the guidelines from Haddock library; - The corrected one using the pdb\_selaltloc tool; ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/cedd64038bf0ad424b65ddb2397ec77145a7ed90.png) Is it possible to help me? I hope I sent you enough information regarding the problem, if not I will surely remedy. Thank you for the attention, and keep up with the good work! Cordially Marco ---
**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:** [May 17, 2024, 12:30pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/2 "2024-05-17T12:30:47Z")
You are missing the 2 next to the + in the atom name ---
**Author:** ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)\ **Post date:** [May 17, 2024, 12:51pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/3 "2024-05-17T12:51:19Z")
Thank you for the fast response Dr. Bovin I just did it, modifying the last PDB: ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/9aee0567f1f6448b3ddf4ec705e9cb99f7c3a8e0.png) (Also the columns seem to be not aligned after the use of the pdb\_tool) It returned me this error, though: “Error in PDB file. Issue when parsing the PDB file at line **1111**. ATOM/HETATM line does not meet the expected format” ---
**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:** [May 17, 2024, 1:03pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/4 "2024-05-17T13:03:07Z")
The PDB format is quite strict. By adding the two you shifted all other columns (clearly visible from the snippet you sent) Delete one space after the 2 you added. ---
**Author:** ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)\ **Post date:** [May 17, 2024, 1:18pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/5 "2024-05-17T13:18:00Z")
Yeah, it seems to work now, thank you very much. One last thing: Is it normal that the last line: TER 1111 GLN A 153 has been swapped with the following one: TER 1113 CU2 A 202 ? Also the conects are gone. ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/32758a14053b488c0d1a4d5279e902f873d69c2c.png) ---
**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:** [May 17, 2024, 2:26pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/6 "2024-05-17T14:26:31Z")
CONECT are irrelevant for HADDOCK And don’t worry about the TER lines. This is a correct behaviour ---
**Author:** ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)\ **Post date:** [May 19, 2024, 5:50pm UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/7 "2024-05-19T17:50:01Z")
Thank you very much for your help, Dr. Bonvin!! ---
**Author:** ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)\ **Post date:** [June 26, 2024, 8:00am UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/8 "2024-06-26T08:00:35Z")
Hello, is it possible that the pdb\_selaltloc tool change ions charges? I’m comparing the pdb structures before and after having used the tool, and the zinc ion charge changed from +2 to +1, even if the copper ion charge remained +2. I noticed that using MOE software, protein-\>properties-\>esemble residue charge Tha’s the pdb before: ATOM 1108 OE1 GLN A 153 50.819 4.796 5.554 1.00 27.09 O ATOM 1109 NE2 GLN A 153 50.228 2.700 4.908 1.00 33.93 N ATOM 1110 OXT GLN A 153 50.916 2.972 10.999 1.00 22.53 O1- TER 1111 GLN A 153 HETATM 1112 ZN+2ZN2 A 201 38.320 16.114 32.936 1.00 18.06 ZN2+ HETATM 1113 CU+2CU2 A 202 40.908 19.845 28.000 1.00 23.14 CU2+ CONECT 420 1064 CONECT 1064 420 END Tha’s the one after selaltloc ATOM 1108 OE1 GLN A 153 50.819 4.796 5.554 1.00 27.09 O ATOM 1109 NE2 GLN A 153 50.228 2.700 4.908 1.00 33.93 N ATOM 1110 OXT GLN A 153 50.916 2.972 10.999 1.00 22.53 O HETATM 1111 ZN+ ZN2 A 201 38.320 16.114 32.936 1.00 18.06 ZN HETATM 1112 CU+ CU2 A 202 40.908 19.845 28.000 1.00 23.14 CU TER 1113 CU2 A 202 END I don’t notice difference or informations about charge reading those pdb lines (In fact I used MOE to do that). if that’s normal, do you know how to manually recover the +2 zinc charge, modifying the pdb? Thank you very much Have a nice day Marco ---
**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:** [June 26, 2024, 8:34am UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/9 "2024-06-26T08:34:26Z")
Looks like a “feature” to me … You could open an issue in the pdb-tools git repo ---
**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:** [June 26, 2024, 8:35am UTC](https://ask.bioexcel.eu/t/haddock-error-uploding-a-pdb-file-with-metals/5016/10 "2024-06-26T08:35:41Z")
PS: indeed simple editing can fix this