Problem with the CNS executable

HADDOCK
1

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) 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

2

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

3

Try to copy your CNS executable directly to the protocols/ folder of your HADDOCK instalation

$ cp /home/software/cns/cns_solve-1.31-UU-Linux64bits.exe /home/qnt/drorimi2/software/haddock2.4-2023-01/protocols/cns1
4

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

5

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?

6

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?

7

You need to recompile CNS with the code provided together with HADDOCK (check the cns1.3 directory)

8

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

9

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

10

Thank you
it worked

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