Installation is successful but Rosetta is not running! #73
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I have installed rosetta in my linux (Ubuntu 20.04) system by following the installation guide mentioned in the website. However, the program is not running with the command rosettaDNA.static.linuxgccrelease @arg. Even the test for compilation did not run because of the FileNotFoundError. Although, g++ is present in user/bin/g++, the compiler compatibility test shows g++ is not found. |
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Replies: 8 comments 1 reply
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Could you paste the error message you got after running Rosetta? This would be helpful. Overall, I see three possible reasons:
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Here is the error message. soumya@soumya-CELSIUS-R970:~/Downloads/rosetta.source.release-371/main/tests/integration/tests/dna_interface_design$ rosettaDNA.static.linuxgccrelease @ I am trying to change the specificity of a protein so that it binds to a desired DNA sequence. For this, I am following the protocol mentioned below. Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with Rosetta. Methods Mol Biol. 2014;1123:265-82. doi: 10.1007/978-1-62703-968-0_17. PMID: 24510272. I am trying to run a demo test first as given in the rosettaDNA applications on the Rosetta website (https://docs.rosettacommons.org/docs/latest/application_documentation/design/rosetta-dna) Even a terminal opened through the rosetta_scrpits/RosettaDNA directory, I am getting the command not found error. Yes, the design.flags file is in the same directory. Here is the information on the available gcc. How do I run the program? Please help out. |
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You probably should be using LigandMPNN for the redesign (https://github.com/dauparas/LigandMPNN), the success rates will be better. Good luck. |
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Generally speaking, the Rosetta commands aren't added to your general path. So you'll have to explicitly provide the full path to the command when you run. So instead of
try
Depending on where/how you installed Rosetta, the path might be different. You can always do a
To see if the application is installed in that path. Note also that depending on how Rosetta was compiled, the name of the executable may be different. It could be rosettaDNA.default.linuxgccrelease or rosettaDNA.default.macclangrelease or something else. The first part of the application name is always the same, but the second two bits can be different depending on the exact compilation details. (Generally static versus default, clang versus gcc versus icc, and linux versus mac doesn't really matter. The key differences for most users are debug versus release, and things like |
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Yes, I followed your instructions and here is the new error message. (base) soumya@soumya-CELSIUS-R970:~$ ls [ ERROR ]: Caught exception: File: src/utility/options/OptionCollection.cc:572 AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. Here are the contents of the ROSETTA_CRASH.log for your reference. #Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/ or use the script Rosetta/main/source/scripts/python/public/report_crashes.py [START_CRASH_REPORT] [END_OPTIONS] /home/soumya/Downloads/rosetta.source.release-371/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libutility.so(backtrace_stringabi:cxx11+0x5a) [0x7a63c2fab35a] [END_BACKTRACE] [START_MESSAGE] [END_MESSAGE] How do I go about with this now? |
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The relevant error message is When you specify Generally speaking, when you run Rosetta you should |
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Thank you so much! It is working now. Also, can you please help me with generating a score file that gives the binding energy and other important parameters? |
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Most Rosetta runs should automatically output a scorefile with the relevant data in it. If you're looking for binding energy specifically, the typical application for protein-protein energy is the InterfaceAnalyzer -- I don't know how well that will work with DNA complexes, though. (It might - I've never tried it. You may want to adjust the energy function used, though.) A better bet might be to look through the related literature and see how the person who originally developed the protocol did the post-analysis. |
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Marking this as "closed", as I hope your question has been answered. If that assessment is incorrect, feel free to re-open or open up a new discussion with more details. |
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The relevant error message is
Option file open failed for: 'design.flags'When you specify
@design.flagson the command line, you're telling Rosetta that there's a file nameddesign.flagsin the current directory which it should open and read the options from.Generally speaking, when you run Rosetta you should
cdinto the "working directory" for the project which contains all your input file and where you want the output files to go. (There's some flexibility, in that you can specify relative paths, but the general concept is that you should be in your "base" directory for that particular project - the one where all your working files are relative to - before you launch Rosetta.)