# Error in the topology generation: prot\_psf\_A could not be created

**URL:** <https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-a-could-not-be-created/125>\
**Category:** HADDOCK\
**Created:** [June 10, 2016, 7:16am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-a-could-not-be-created/125 "2016-06-10T07:16:56Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![factored](https://avatars.discourse-cdn.com/v4/letter/f/ccd318/32.png) [@factored](https://ask.bioexcel.eu/u/factored)\
**Post date:** [June 10, 2016, 7:16am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-a-could-not-be-created/125/1 "2016-06-10T07:16:56Z")

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I am using 2 proteins from the DBD5 which I have run through the simple interface on the haddock server which finishes a complete analysis.

On my local copy of haddock using the exact same protein files and residues, haddock errors with the following:  
Error in the topology generation: prot\_psf\_A could not be created

I have run pdb\_format.py on the files from the git repository and both seem fine and there is nothing I can determine from the generate\_A/B.out files. They end like this:

ASSFIL: file ligand.pep opened.  
CHAIN\> coordinates @@$coor\_infile  
%ASSFIL-ERR: error opening file .//data/sequence/protein1.pdb  
%ASSFIL error encountered: Error accessing file  
(CNS is in mode: SET ABORT=NORMal END)

* * *

ABORT mode will terminate program execution.

* * *

Program will stop immediately.  
…

On a side note, there seems to be 2 run.cns parameters required for a local haddock run which are not in the run.cns downloaded from a serverrun, specifically:  
{===\>} clust\_meth=“FCC”;  
{===\>} clust\_cutoff=0.75;

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**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 10, 2016, 7:31am UTC](https://ask.bioexcel.eu/t/error-in-the-topology-generation-prot-psf-a-could-not-be-created/125/2 "2016-06-10T07:31:11Z")

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The error message is pretty clear: protein1.pdb not found - you have an error in your path definitions… Compare new.html and run.cns with the one from an example or from a server run.

As for the FCC question: nothing is missing, you probably are using instead RMSD clustering.