# Error in the topology generation: prot\_psf\_mol2 could not be created
**URL:** https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341
**Category:** HADDOCK
**Created:** [November 22, 2024, 6:02pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341 "2024-11-22T18:02:29Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@acr0116](https://ask.bioexcel.eu/u/acr0116)
#### Post date: [November 22, 2024, 6:02pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341/1 "2024-11-22T18:02:29Z")
I am trying to run haddock2.5 locally, I have it installed on a liunuc HPC cluster. I. am trying to run the protein-protein example with E2A and HPR. It seems to create run1/ correctly and when i run haddock2.5 again inside run1/ it begins but stops with “Error in the topology generation: prot\_psf\_mol2 could not be created”
The begin/ directory has:
begin]$ ls
e2aP\_1F3G.psf e2aP\_1F3G.psf\_1 file\_1.list generate\_1.out generate\_2.out iteration.cns
and the bottom of generate\_2.out has:
if ( &convert = true ) then
NEXTCD: condition evaluated as false
COOR\> convert=true
COOR\> end if
COOR\> @@$file
ASSFIL: file hpr\_1.pdb opened.
%COOR-ERR: unrecognized command:
show
^^^^
which propogates many times and results in:
NEXTCD: condition evaluated as true
%COOR-ERR: unrecognized command:
identity
^^^^^^^^
%PARSER error encountered: Encountered too many parsing errors.
(CNS is in mode: SET ABORT=NORMal END)
* * *
ABORT mode will terminate program execution.
* * *
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 9857944 bytes
Maximum dynamic memory overhead: 1040 bytes
Program started at: 11:47:11 on 22-Nov-2024
Program stopped at: 11:47:11 on 22-Nov-2024
CPU time used: 0.1352 seconds
============================================================
at the bottom. generate\_1.out seems to be fine.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [November 22, 2024, 9:24pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341/2 "2024-11-22T21:24:31Z")
How did you run the example?
Directly from the example dir of your haddock2.5 installation?
Something seems wrong.
---
### Author:  [@acr0116](https://ask.bioexcel.eu/u/acr0116)
#### Post date: [November 22, 2024, 9:47pm UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341/3 "2024-11-22T21:47:33Z")
Yes I ran it directly from the example directory provided with the haddock2.5 distribution. I am getting similar errors trying to set up my own run in a separate directory.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [November 23, 2024, 6:33am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341/4 "2024-11-23T06:33:08Z")
Describe exactly the steps you are taking.
Did you try using the executable provided in the distribution email? pre-complied for Linux
Something is wrong on your side as haddock2.5 works perfectly fine on our side (it is now powering the HADDOCK server)
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [November 23, 2024, 6:51am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-mol2-could-not-be-created/5341/5 "2024-11-23T06:51:47Z")
PS: Possibly share with us a full archive of the failing run