# Problem with the CNS executable **URL:** \ **Category:** HADDOCK\ **Created:** [June 5, 2023, 8:54am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364 "2023-06-05T08:54:18Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [June 5, 2023, 8:54am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/1 "2023-06-05T08:54:18Z")
Hi I have this error when trying to run local version of haddock There is a problem with the CNS executable defined in run.cns: ./protocols/cns1: Command not found. I followed all the cns download rules for haddock3 (from the link [CNS Installation — haddock3 3.0.0 documentation](https://www.bonvinlab.org/haddock3/CNS.html)) and when I typed in cns it gave the correct output And I changed the file to my cns location in the file config.local set CNSTMP=/home/software/cns/cns\_solve-1.31-UU-Linux64bits.exe set QUEUETMP=/bin/csh set NUMJOB=4 set QUEUESUB=QueueSubmit\_concat.py what am I missing? I made a new directory named sh3\_qkc in the directory /home/qnt/drorimi2/software/haddock2.4-2023-01/ ran haddock2.4, then when in to the file run1 and wrote haddock2.4 and the error came up. was I also supposed to change the location in the file run.cns? or do something else? Thank you very much! Miriam ---
**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 5, 2023, 9:08am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/2 "2023-06-05T09:08:54Z")
This does not seem a haddock3 issue, but rather a haddock2.X one. Did you run the install.csh script after editing the config.local file? And before doing that, remove if present the protocols/cns1 file ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [June 5, 2023, 9:44am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/3 "2023-06-05T09:44:20Z")
Try to copy your CNS executable directly to the `protocols/` folder of your HADDOCK instalation ```bash $ cp /home/software/cns/cns_solve-1.31-UU-Linux64bits.exe /home/qnt/drorimi2/software/haddock2.4-2023-01/protocols/cns1 ``` ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [June 5, 2023, 11:08am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/4 "2023-06-05T11:08:38Z")
thank you now the error is waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/sh3\_qkc/run1/begin/sh3.pdb… waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/sh3\_qkc/run1/begin/sh3.psf… waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/sh3\_qkc/run1/begin/mc\_qrppvppkpkwlc.psf… waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/sh3\_qkc/run1/begin/mc\_qrppvppkpkwlc.pdb… Error in the topology generation: prot\_psf\_mol1 could not be created Thx, Miriam ---
**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 5, 2023, 11:21am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/5 "2023-06-05T11:21:00Z")
Could still be CNS-related. Check the .out files in the begin directory for errors. Start at the bottom of those. Did you first try to run a provided example? ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [June 5, 2023, 11:34am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/6 "2023-06-05T11:34:21Z")
when trying the protein-peptide example run I encountered the same error waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/examples/protein-peptide/run1/begin/1NX1\_protein.pdb… waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/examples/protein-peptide/run1/begin/1NX1\_protein.psf… waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/examples/protein-peptide/run1/begin/DAIDALSSDFT\_ext.psf… waiting for /home/qnt/drorimi2/software/haddock2.4-2023-01/examples/protein-peptide/run1/begin/DAIDALSSDFT\_ext.pdb… Error in the topology generation: prot\_psf\_mol1 could not be created =\> HADDOCK stopped the generate\_1.out file ends like this RTFRDR\>set message=off echo=off end %AUTOAN error encountered: exceeded MXRTT (RTF) parameter → recompile program (CNS is in mode: SET ABORT=NORMal END) * * * ABORT mode will terminate program execution. * * * Program will stop immediately. ============================ what does this mean? ---
**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 5, 2023, 11:47am UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/7 "2023-06-05T11:47:39Z")
You need to recompile CNS with the code provided together with HADDOCK (check the cns1.3 directory) ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [June 5, 2023, 12:23pm UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/8 "2023-06-05T12:23:42Z")
OK what I did to move the files of haddock cns to the cns source file was as followes: cp /home/qnt/drorimi2/software/haddock2.4-2023-01/cns1.3/\* source/ (and not what it said on the website since Im using haddock2.4 and not 3 so I cant do cp ~/software/haddock3/varia/cns1.3/\* source/ since its not in the right directory) is this incorrect? and thats why when I did the recompile it did not work properly? thank you ---
**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 5, 2023, 3:07pm UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/9 "2023-06-05T15:07:57Z")
And did you reinstall / recompile CNS after that? Was it successful? Of course the exact commands of the tutorial can not be used as your installation directories are different ---
**Author:** ![Miriam](https://avatars.discourse-cdn.com/v4/letter/m/c89c15/32.png) [@Miriam](https://ask.bioexcel.eu/u/Miriam)\ **Post date:** [June 5, 2023, 7:21pm UTC](https://ask.bioexcel.eu/t/problem-with-the-cns-executable/4364/10 "2023-06-05T19:21:42Z")
Thank you it worked