# Error in the topology generation **URL:** \ **Category:** HADDOCK\ **Created:** [April 21, 2016, 9:14am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64 "2016-04-21T09:14:49Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![strumillo](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/strumillo/32/44_2.png) [@strumillo](https://ask.bioexcel.eu/u/strumillo)\ **Post date:** [April 21, 2016, 9:14am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/1 "2016-04-21T09:14:49Z")
Hello, I am submitting my own pdb files, and I get the following error: Error in the topology generation: prot\_psf\_A could not be created I removed all the HETATM from the pdb file, it ends up with END, doesnt have the segid. What else could be wrong with that pdb? ---
**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\ **Post date:** [April 21, 2016, 9:47am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/2 "2016-04-21T09:47:15Z")
Hello, Without seeing the PDB it can only be a guess but could it be that your PDB contains modified amino-acids ? They are still labelled as “ATOM” but are not supported by HADDOCK (the list of modified amino-acid supported by HADDOCK is available here: [http://haddock.science.uu.nl/services/HADDOCK/library.html](http://haddock.science.uu.nl/services/HADDOCK/library.html)) ---
**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:** [April 21, 2016, 10:08am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/3 "2016-04-21T10:08:35Z")
You can check the correct formatting of your PDB file using our pdb\_format.py script from our pdb-tools GitHub repository: > **[haddocking/pdb-tools](https://github.com/haddocking/pdb-tools)** > > A dependency-free cross-platform swiss army knife for PDB files. - haddocking/pdb-tools E.g.: ```auto pdb_format.py ``` ---
**Author:** ![strumillo](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/strumillo/32/44_2.png) [@strumillo](https://ask.bioexcel.eu/u/strumillo)\ **Post date:** [April 21, 2016, 2:13pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/4 "2016-04-21T14:13:47Z")
It _seems_ everything is OK. I got _this_ outcome 😉 ---
**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:** [April 21, 2016, 2:29pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/5 "2016-04-21T14:29:15Z")
If this problem persists, do inspect the content of the generate\_A.our file in the begin directory and start looking for error messages at the bottom of that file. Are you running a local version? ---
**Author:** ![strumillo](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/strumillo/32/44_2.png) [@strumillo](https://ask.bioexcel.eu/u/strumillo)\ **Post date:** [April 21, 2016, 2:41pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/6 "2016-04-21T14:41:35Z")
BINGO! 5098 %GENRES-ERR: residue TPO not found in topology files. Add topology definition. Thank you! ---
**Author:** ![Adrimel](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adrimel/32/40_2.png) [@Adrimel](https://ask.bioexcel.eu/u/Adrimel)\ **Post date:** [April 21, 2016, 2:58pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/7 "2016-04-21T14:58:16Z")
In the list of modified amino acids supported by HADDOCK, you can find ```auto TOP: phosphorylated THR. Atoms: N,HN,CA,HA,CB,HB1,HB2,OG P,O1P,O2P,O3P,CG2,HG21,HG22,HG23,C,O ``` See: [http://haddock.science.uu.nl/services/HADDOCK2.2/library.html](http://haddock.science.uu.nl/services/HADDOCK2.2/library.html) So do change the name of that residue in your PDB file ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 18, 2017, 12:30pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/8 "2017-12-18T12:30:07Z")
hello there, I am submitting my own PDB files, one of them showing error during generation of `.out` files `%GENRES-ERR: residue UNK not found in topology files. Add topology definition.` But I want to do protein-protein docking with this drug bind to it. Is there any possibility??? ---
**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\ **Post date:** [December 18, 2017, 12:46pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/9 "2017-12-18T12:46:17Z")
Hello, If you look at this page: [http://haddock.science.uu.nl/services/HADDOCK2.2/library.html](http://haddock.science.uu.nl/services/HADDOCK2.2/library.html) You’ll see that co-factors must be defined as HETATM to get their topologies obtained from PRODRG. ---
**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:** [December 18, 2017, 12:47pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/10 "2017-12-18T12:47:22Z")
Using our web server? Co-factors and small ligands should be defined as HETATM instead to ATOM ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 18, 2017, 1:36pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/11 "2017-12-18T13:36:34Z")
No, I am using software haddock2.2. Can we modify the topology files? Please help me in this regard!!! ---
**Author:** ![joaor](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaor/32/194_2.png) [@joaor](https://ask.bioexcel.eu/u/joaor)\ **Post date:** [December 18, 2017, 2:15pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/12 "2017-12-18T14:15:53Z")
The local version of HADDOCK is definitely not user-friendly, thus the existence of the web server. If you have 3-4 core developers telling you to use the server, you should listen. You haven’t given us a good reason as to why you want to use the local version. If you want to add a new molecule/residue to the topology, you’re in for a lot of work. You need to use an external software that calculates exactly what the bonds, angles, partial charges, etc are. It’s _not_ simple. Please, do give another try to the webserver. You’re wasting your own time trying to fix all of these issues when you could be analyzing your runs… ---
**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:** [December 18, 2017, 2:27pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation/64/13 "2017-12-18T14:27:47Z")
Reading the online manual might also help… [http://www.bonvinlab.org/software/haddock2.2/faq/#ligand](http://www.bonvinlab.org/software/haddock2.2/faq/#ligand)