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rosetta backrub

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rosetta backrub


I want to use Rosetta backrub for peptide design. by I faced an error that I think it caused to incompatible .py and .sh files and Rosetta 3.9 2018 version. I searched a lot on Rosetta website to find out any example of .py and .sh file that they need for running Rosetta Backrub. my error was ERROR: unable to open MM atom type  set file:/home/nanobio/amin/rosetta_database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt ERRoR: Exit from: src/core/chemical/ line 64".

 Another weird thing that happened to me was the name of _last.pdb and _low.pdb files. these files generated but with a weird name that combination of two pep_7 numbering like" pep7_R_0001pep7_R_0003_last.pdb"

I will attach you all of my running file please help me what is my problem and how I can solve it. 

for attach .sh file I must change .sh file to .txt.


AttachmentSize KB
pep7_R.pdb19.96 KB
backrub.txt1.03 KB
Post Situation: 
Thu, 2018-10-04 08:01

Hi Ladan,

Can you also attach the log from Rosetta? Meaning, when you run Rosetta, everything that prints out leading up to the error message "ERROR: unable to open..."

This will help me figure out exactly what's going wrong.




Fri, 2018-10-05 11:22

Hi Amanda

I am so sorry for answering you too late because the power&nbsp;of my server broken out so I could not access my server. so I try to set another server to work with that has a different version of Rosetta&nbsp;that I worked with. This version is&nbsp;rosetta_bin_linux_2018.33.60351_bundle. Now I had a different problem my PDB file cannot read by Rosetta and my run finished in the first step. I set all of the things&nbsp;I do not know what is happened. The error is "No start PDB file specified". I will set you my&nbsp;.py file and my PDB file. would you mind introducing me what was happened?

thanks so much

File attachments: 
Mon, 2018-10-15 12:46


The problem is actually explained in file.  If you open your file and search for the error you got "No start PDB file specified" you will see that's on line 53. That code block is:

# Determine the starting PDB structure from either the PDB_PATH environment
# variable, or the first command line argument
if os.environ.has_key("/home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/pep7_R.pdb"):
    pdb_path = os.path.abspath(os.environ["/home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/pep7_R.pdb"])
elif len(sys.argv) >= 2:
    pdb_path = os.path.abspath(sys.argv[1])
    sys.exit("No start PDB file specified")

The script is failing both the if and the elif and going to the else. Rather than setting an environment variable, I would recommend using the system argument from the elif which means running the python script like this: 

python /home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/pep7_R.pdb

when I did that, i got the following output:

/home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/backrub.static.linuxgccrelease -database /home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/database -s /netapp/home/aloshbau/benchmarks/ladimafakher/pep7_R.pdb -ignore_unrecognized_res -ex1 -ex2 -extrachi_cutoff 0 -out:prefix pep7_R_0001 -mute -backrub:ntrials 10000 -score:weights pre_talaris_2013_standard.wts -score:patch score12 -out:nstruct 10

which you can then copy/paste and run in your terminal to start Rosetta.

And then the script continues on to try to submit the above command to your your cluster. This probably won't work because the script is written for the UCSF cluster. If you only have a couple jobs and it's not submitting correctly, you can copy/paste the command into your own terminal. Otherwise you will have to adapt the submission part to match your own cluster, which you would probably need to talk to your local cluster adminstrators because I won't know how your cluster works. Note at the very beginning of the python script there's the warning:

"# These are Sun Grid Engine options used on the UCSF cluster, some may need to
# be changed for your local environment"

This is why you'd need to adapt the script since the python script is an interface between your cluster and Rosetta. However if you're just running a couple jobs and want to run them on your own laptop/computer and don't need anything to do with a cluster/server/supercomputer, you can use the Rosetta command printed out by the python script in your own terminal.

Regarding that command, it's a little dated (not sure where the python script is from) in terms of the score weights/patches, those are no longer needed. The database flag is also no longer needed. The following command should work and use the CURRENT score function:

/home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/backrub.static.linuxgccrelease -s /netapp/home/aloshbau/benchmarks/ladimafakher/pep7_R.pdb -ignore_unrecognized_res -ex1 -ex2 -extrachi_cutoff 0 -out:prefix pep7_R_0001 -mute -backrub:ntrials 10000 -out:nstruct 10

And then it's very important to save the log of your Rosetta run so use ">> however_you_label_your_files.log" like this one you are ready to do your production run:

/home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/backrub.static.linuxgccrelease -s /netapp/home/aloshbau/benchmarks/ladimafakher/pep7_R.pdb -ignore_unrecognized_res -ex1 -ex2 -extrachi_cutoff 0 -out:prefix pep7_R_0001 -mute -backrub:ntrials 10000 -out:nstruct 10 >> however_you_label_your_files.log

Options for modifying this command line can be found here:

Hope that helps! Please don't hesitate to ask me any more questions about anything.

Best regards,


Sun, 2018-10-21 16:13

Hi Amanda

I really thank you for helping me. I used your commands that you sent me in the previous message"/home/sziaee/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/backrub.static.linuxgccrelease -s /netapp/home/aloshbau/benchmarks/ladimafakher/pep7_R.pdb -ignore_unrecognized_res -ex1 -ex2 -extrachi_cutoff 0 -out:prefix pep7_R_0001 -mute -backrub:ntrials 10000 -out:nstruct 10 >> " and Rosetta ran but after several minutes it finished without any error. the file generated but I could not see any table which contained suggested sequences like as see on Rosie server.  the ten model_stripped_0001 low and last pbd were generated too. what is the problem? would you mind helping me in this issue?

I will send you .log file that generated as you said. 

I will send you .sc file  but I renamed it to  .txt

thanks a lot

Thu, 2018-11-01 03:47