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The problem has been solved



Not a question, but a note of an issue to save anyone getting lost by it

I had a spot of bother installing PyRosetta on a cluster running Ubuntu as PyRosetta was giving:

lib64/ version `GLIBC_2.27' not found

(Dejavu of pytorch, anyone?)
To fix it the system environment CONDA_OVERRIDE_GLIBC=2.27 does the trick:

Post Situation: 

[LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.

Loop Modeling


I am trying to use the LoopModelerMover to relax a couple of loops in a protein complex. I would like to let Rosetta select cutpoints automatically so I leave the cutpoints set to 0. An example script is attached as a text file. I have tried specifying the loops as loop subtags and as a loops file, and in both cases I get this error. 

ERROR: Can't build a fold tree from a loop with an unspecified cut point.


Post Situation: 

getting a3m files

Structure prediction


I want to use RoseTTAfold on the server but it requires an a3m file I dont know how to generate.

I saw a script on the github page ( that to my understanding is supposed to convert fasta to a3m but it dosent seem to work and I get the following error:

Post Situation: 

C-termini remodelling of dimeric structure removes second chain

Loop Modeling

Dear Rosetta Community,

I am trying to remodel a short C-terminal loop into  a docked dimeric structure consisting of 2 identical proteins and while the modeling itself worked, the output contains only the first protein.  The flags I used are the following:
-in:file:s bestp1.pdb
-remodel:blueprint c-term.remodel
-no_optH false
-remodel:num_trajectory 1

Post Situation: 

Rosetta Enzyme design cst block raises error

Enzyme Design

Hi All,

I'm trying to run the Rosetta Enzyme Design protocol and I wrote a cst file for the matching step.

My cst file includes two blocks (I pasted below), they use the exactly same format but when I add the second block the match program starts to report an error.

Post Situation: 

Compilation and unit test failures


Hi all,

I installed Rosetta 3.13 in KISTI supercomputor 5 (Nurion) (

And, I ran the unit tests. It is showing 85% success rate. 

Below is what I did and I have attached the relevant documents.

$ cd rosetta/main/source

$ module purge

$ module load craype-network-opa python/2.7.15 gcc/8.3.0 mvapich2/2.3.1 craype-mic-knl

Post Situation: 

Internal error while running AbinitioRelax

Structure prediction

I am trying to learn Rosetta without any background computer science or bioinformatics. I tried to run the AbinitioRelax.default.linuxrelease program with the proper input files and got the following internal error -

[FILE]: src/core/chemical/
[LINE]: 149
[ ERROR ] UtilityExitException
ERROR: Unable to open file: /home/rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt


Post Situation: 

Rosetta Double changing mmCIF chain ID


Hi everyone!

Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?

Best and thank for any help,


Post Situation: 


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