CNS error: permission denied

HADDOCK
1

Hi everyone!

I’m having a problem when I run HADDOCK locally. I have installed CNS and it seems to be working, when I type cns in the terminal line here is what I’m seeing:

          ============================================================
          |                                                          |
          |            Crystallography & NMR System (CNS)            |
          |                         CNSsolve                         |
          |                                                          |
          ============================================================
           Version: 1.3
           Status: General release
          ============================================================
           Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
                       P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn,
                       J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
                       L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren.
           Copyright (c) 1997-2010 Yale University
          ============================================================
           Running on machine: hostname unknown (Mac/Intel,64-bit)
                               with  8 threads
           Program started by: marion
           Program started at: 17:20:54 on 12-Apr-2023
          ============================================================

 FFT3C: Using FFTPACK4.1

CNSsolve>

However, when I run haddock2.4 in my run1 folder, this is the output:

There is a problem with the CNS executable defined in run.cns:

./protocols/cns1: Permission denied.


=> HADDOCK stopped

I have tried uninstall and reinstall CNS, I have given all the permissions necessary. Not sure what to do here, any help?

Thank you very much,
Marion.

2

Try deleting cns1 from the protocols directory in your haddock installation / runs

And make sure to define the full path to the cns exec in run.cns and not only the directory where it resides

3

Thanks Prof. Bonvin, the problem was with the path to the CNS exec in the run.cns.

In case someone else also has this problem, here is an easy way to fix it:

  1. Go to your cns directory
  2. Source cns_solve_env file
  3. Type which cns in terminal
  4. Copy that path into your run.cns file
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