Hi everyone,
I downloaded Haddock2.4, and I am trying the installation as suggested in the haddock manual
I changed the config.local file to specify the location of my cns executable.
However, when I try to run the install.csh with the config .local I get the following error:
Setting up QueueSubmit to QueueSubmit_concat.py
POSTPROCESS: Undefined variable.
Can someone help me?
Thanks,
Simonbis
Hi Simonbis
Which version of HADDOCK2.4 do you have?
If the July release, simply try downloading it again.
There was an issue with the install.csh script
Dear Prof. Bonvin,
Thanks for your prompt reply.
As you suggested, I downloaded the most recent version of Haddock2.4 and the installation worked fine.
I tried to run some of the tests included in the Haddock2.4 package (e.g. haddock2.4-2020-07/tests/protein-protein, haddock2.4-2020-07/tests/protein-ligand, haddock2.4-2020-07/tests/protein-dna). In all cases Haddock is able to generate the run1 folder with the run.cns file. I did not change anything in the run.cns file and I just I run again haddock2.4. I got this error:
Error in the topology generation: prot_psf_mol1 could not be created
=> HADDOCK stopped
Best,
Simonbis
Make sure you have the correct definition of the path to the CNS executable.
Is your CNS executable working?
The path to the CNS executable is correct. Below you can see what is reported in the the cns.run file:
{===>} queue_1="/bin/csh";
{===>} cns_exe_1="/home/ubuntu/Desktop/Programs/CNS/cns_solve_1.3/intel-x86_64bit-linux/bin/cns";
{===>} cpunumber_1=4;
Also my CNS executable works. In fact when if I type in a new terminal /bin/csh and then /home/ubuntu/Desktop/Programs/CNS/cns_solve_1.3/intel-x86_64bit-linux/bin/cns I initiate the CNS software.
Best,
Simone
What is then the content of the begin directory in the created run?
Is it empty? Are there generate_X.out files present?
If this is the case, check at the end of those files for error messages.
If those are not present, then something is still wrong with your CNS definition.
Also try starting a fresh run.
In the run1/begin directory there are two generate_X.out files.
At the end of each file it is reported the following error:
%RTFRDR error encountered: exceeded MXRTRS (RTF) parameter --> recompile program
(CNS is in mode: SET ABORT=NORMal END)
ABORT mode will terminate program execution.
Program will stop immediately.
It seems that the error is due to CNS.
Did you recompile it with the provided files from the cns1.3 directory?
And otherwise I can share with you an executable - email me for that
Hello, I am presently having the same issue.
Is there any description on how to solve it?
Thank you in advance for your availability!
Check the CNS installation instructions at:
https://www.bonvinlab.org/haddock3/CNS.html
Importantly, when compiling with gfortran (recommended), make sure to use the options in the Makefile described under:
Hello, thank you for your quick response.
I was following that specific guide, but to no avail.
My conclusion is that the installation wasn’t dealing well with the virtualization process I was using.
I attempt it on an actual linux machine and it worked like a charm!
Note that might be able to use your CNS executable in your virtualised environment without having to recompile it
Thank you so much!!
I’ll save that note for future attempts !