# Error in the topology generation: prot\_psf\_mol2 could not be created on HPC **URL:** \ **Category:** Uncategorized\ **Created:** [August 13, 2025, 3:30pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864 "2025-08-13T15:30:18Z")\ **Posts on this page:** 14\ **Page:** 1
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 13, 2025, 3:30pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/1 "2025-08-13T15:30:18Z")
I got the error when running my job on HPC Haddock 2.5. I have used the json file from the already completed job on web server. And the method I am using is correct as I have got few successfully completed jobs from this local run previously. I just wonder if the parameters worked on web server it should also work locally as well. [2025-08-13 10:57:59] Starting HADDOCK [2025-08-13 10:57:59] HADDOCK version: 2.5 - December 2024 [2025-08-13 10:57:59] Parsing run.cns file [2025-08-13 10:57:59] Parsing run.param in . …. …. …. [2025-08-13 10:57:59] setting some variables: [2025-08-13 10:57:59] HADDOCK\_DIR set to: /opt/haddock2.5-2024-12 [2025-08-13 10:57:59] N\_COMP set to: 2 [2025-08-13 10:57:59] RUN\_NUMBER set to: -test2 [2025-08-13 10:57:59] PDB\_FILE1 set to: ./protein1.pdb.pdb [2025-08-13 10:57:59] PROT\_SEGID\_1 set to: A.pdb [2025-08-13 10:57:59] AMBIG\_TBL set to: ambig.tbl [2025-08-13 10:57:59] UNAMBIG\_TBL set to: unambig.tbl [2025-08-13 10:57:59] PDB\_FILE2 set to: ./protein2.pdb.pdb [2025-08-13 10:57:59] PROT\_SEGID\_2 set to: B.pdb [2025-08-13 10:57:59] HADDOCK\_DIR /opt/haddock2.5-2024-12 [2025-08-13 10:57:59] N\_COMP 2 [2025-08-13 10:57:59] RUN\_NUMBER -test2 [2025-08-13 10:57:59] PDB\_FILE1 ./protein1.pdb.pdb [2025-08-13 10:57:59] PROT\_SEGID\_1 A.pdb [2025-08-13 10:57:59] AMBIG\_TBL ambig.tbl [2025-08-13 10:57:59] UNAMBIG\_TBL unambig.tbl [2025-08-13 10:57:59] PDB\_FILE2 ./protein2.pdb.pdb [2025-08-13 10:57:59] PROT\_SEGID\_2 B.pdb [2025-08-13 10:57:59] Looking for existing files [2025-08-13 10:58:00] waterdock false [2025-08-13 10:58:00] Generating PSF and PDB file of molecule 1 [2025-08-13 10:58:00] Generating PSF and PDB file of molecule 2 [2025-08-13 10:58:01] waiting for the psf files… [2025-08-13 10:58:01] waiting for the psf files… [2025-08-13 10:58:11] waiting for the psf files… [2025-08-13 10:58:11] waiting for the psf files… [2025-08-13 10:58:21] waiting for the psf files… [2025-08-13 10:58:21] waiting for the psf files… [2025-08-13 10:58:32] waiting for the psf files… [2025-08-13 10:58:32] waiting for the psf files… [2025-08-13 10:58:42] waiting for the psf files… [2025-08-13 10:58:42] waiting for the psf files… [2025-08-13 10:58:52] waiting for the psf files… [2025-08-13 10:58:52] waiting for the psf files… [2025-08-13 10:59:02] waiting for the psf files… [2025-08-13 10:59:02] waiting for the psf files… [2025-08-13 10:59:13] waiting for the psf files… [2025-08-13 10:59:13] Error in the topology generation: prot\_psf\_mol2 could not be created [2025-08-13 10:59:13] HADDOCK stopped [2025-08-13 10:59:13] ############################################################################## [2025-08-13 10:59:13] Finishing HADDOCK [2025-08-13 10:59:13] Au revoir. Tot ziens. Bye bye. ---
**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:** [August 13, 2025, 5:43pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/2 "2025-08-13T17:43:07Z")
do you have any ligand in your system? The server will generate topo/param files for those. When running locally you will have to copy those to the toppar directory of your run ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 13, 2025, 6:10pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/3 "2025-08-13T18:10:40Z")
Yes. And the jobs I am able to run locally also contains ligand but I have not done any explicit step to manage toppar. The json causes the error is drived from the following results [HADDOCK results page](https://rascar.science.uu.nl/haddock2.4/result/7439153330/539127-monika_test2) which is completed successfully on web server but throws error on HPC. 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:** [August 13, 2025, 6:23pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/4 "2025-08-13T18:23:10Z")
Then most likely you are missing the ligand topology and parameter files. Those are not included in the json file. ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 13, 2025, 6:42pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/5 "2025-08-13T18:42:40Z")
Ok. So can you please provide me further detail on which step I have to do that and from where I can find these files. I will try to re-run the job with these modifications. 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:** [August 14, 2025, 11:21am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/6 "2025-08-14T11:21:05Z")
If you are docking the same protein as in your server run, you can extract the ligand topo and param files from that run. Look for ligand.param and ligand.top in the toppar directory of that run. And copy those to the run directory you generate on your HPC system before starting the haddock run. They should go into the toppar directory. If you have different proteins/ligands, you will have to generate the parameters for each ligand… You could use the server for this, downloading the files before submission. Or try to use tools like acpype to parametric your ligands. Check also: [bio2byte.be/acpype](http://bio2byte.be/acpype) You will need the files in CNS format. ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 14, 2025, 2:15pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/7 "2025-08-14T14:15:20Z")
Thank you so much for the details and for your prompt responses. Ill implement these steps and update here the status of my run. Thanks ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 14, 2025, 3:18pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/8 "2025-08-14T15:18:08Z")
I have run jobs. I found out that my run directory’s toppar folder already contains these two files. But still I ran one job with the existing ligand files and another by explicitly placing the ligand files although it already contains it. In both the cases it throws the same error. Error in the topology generation: prot\_psf\_mol2 could not be created; I would appreciate your help in this regard. 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:** [August 14, 2025, 6:36pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/9 "2025-08-14T18:36:32Z")
the files present by default are empty Share a run directory if you want us to look at the problem (one where you copied the ligand files) ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 15, 2025, 7:47pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/10 "2025-08-15T19:47:13Z")
Hello, I have sent the run directory to you. please confirm if you have received it. 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:** [August 17, 2025, 7:49am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/11 "2025-08-17T07:49:42Z")
nothing - also not in the spam ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 18, 2025, 2:21pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/12 "2025-08-18T14:21:26Z")
Please send me the email ID to resend it. 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:** [August 19, 2025, 8:46am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/13 "2025-08-19T08:46:16Z")
You should be able to find my university email 🙂 ---
**Author:** ![fow028](https://avatars.discourse-cdn.com/v4/letter/f/b38774/32.png) [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Post date:** [August 19, 2025, 2:21pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created-on-hpc/5864/14 "2025-08-19T14:21:59Z")
Sent. Thanks