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Rosetta Enzyme design cst block raises error

Category: 
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

Category: 
Compilation

Hi all,

I installed Rosetta 3.13 in KISTI supercomputor 5 (Nurion) (https://www.ksc.re.kr/eng/index/main).

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

Category: 
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/GlobalResidueTypeSet.cc
[LINE]: 149
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to open file: /home/rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt


[END_MESSAGE]
[END_CRASH_REPORT]
 

Post Situation: 

Rosetta Double changing mmCIF chain ID

Category: 
Design

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,

Victor

Post Situation: 

r_frag_quality

Category: 
Fragment Generation

Hi everyone,

I would like to assess my designs using the fragment quality metric and biased forward folding. In both cases Rosetta documentation suggests to use the r_frag_quality application. However I cannot find it in my locally compiled versions of rosetta (for example in rosetta_src_2020.08.61146_bundle). Can anybody help? 

Thanks

 

 

Post Situation: 

arm64 processor is not supported for new M1 chip

Category: 
Compilation

Hello,

I'm fairly new to dealing with these kinds of software installation and compilation. I want to download the latest release of rosetta on my M1 Macbook air laptop and I've run into the following problem when I try to compile the rosetta bundle in the Rosetta/main/source directory:

source % ./scons.py -j6 mode=release bin

scons: Reading SConscript files ...

Traceback (most recent call last):

  File "/Users/martinfe/Rosetta/main/source/SConstruct", line 183, in main

Post Situation: 

RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()

Category: 
Docking

Dear Rosetta Users, 

I am trying to generate 20000 structures by using RosettaLigand, but the application keeps on crashing with the following errors:

[FILE]: src/core/conformation/util.cc

[LINE]: 654

[START_MESSAGE]

[ ERROR ] UtilityExitException

Post Situation: 

clean_pdb.py

Category: 
Structure prediction

Hi guys,

I just installed Rosetta in my Mac and trying to do the ResettaCM following the tutorials (https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial). when i do the first step: Rosetta/demos/tutorials/rosetta_cm/scripts/clean_pdb.py 2RH1_ISOLATED A

Post Situation: 

MPI optimization on TACC stampede2 HPC

Category: 
Structure prediction
Loop Modeling
Symmetry
Membrane

Dear community,

I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.

Post Situation: 

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