Can't execute ana_structures.csh

HADDOCK
1

Hello everyone,

I am a new user of the local version of Haddock2.4. I successfully finished the docking calculations by following the local docking tutorial, but I am stuck in the analysis section because I can’t execute the ana_structures.csh script. Every time I execute it the following message appears: “If: Missing file name”. I am running haddock in a ubuntu 18.04 machine. Could somebody help me a little with this? I am a bit lost.

Thanks,
Gabriel

2

Do you have csh and tcsh installed on your system?

Would also be good to get more info… E.g. when you run it, what are the most recent files created.

3

Hello,

Thank you for your reply. Yes, I have csh/tcsh installed on my system. I am trying to analyze the results provided in the tutorial (https://surfdrive.surf.nl/files/index.php/s/sf2FUVau1Iasocd). I also run the example in my computer and try to analyze it but the same error appeared.

UPDATE: the script successfully generate the following files before it fails: file.nam_Edesolv, file.nam_dH, file.nam_viol, file.nam_ener, file.nam_bsa and file.nam_haddock-score. structures_haddock-sorted.stat is not generated. By looking the script, I think the problem may be related with the RMSD section.

Thanks again,
Gabriel

4

Since you are not providing more information, I’d say try a few things: make sure you followed all the steps before, could be a good idea to run it again. Also, try to understand what this tools is doing, are you executing it from the correct location? If you get lost, maybe try running one of the basic tutorials first.

5

Hello,

I am analyzing the result files of a pre-executed run provided by the tutorial, so I don’t think my problem is related with the docking run itself.

I understand that this script extracts text of each pdb file generated during the docking and arrange it into a dataframe structure, so I am executing the script from the it1/water folder.

Thanks,
Gabriel

6

Ok I think I solved it. For some reason that I still can’t understand, the "setenv PROFIT which profit" (line 21) is not executing correctly even though $found==1 (PROFIT is found). I fixed it by adding the line ""setenv PROFIT which profit" outside the loop (after line 94 of the script) and everything seems to be generated correctly.

Thanks a lot for your comments,
Gabriel