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mpirun docking_protocol

Submitted by NanB on Mon, 2020-08-03 11:38
Category: 
Docking

Hi all,

I was running mpi docking_protocol (docking_protocol.cxx11threadmpiserialization.linuxgccrelease) to generate 500 decoys. I got this error and only 470 decoys as output:

[ ERROR ]: Error(s) were encountered when running jobs.
12 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

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Rosetta 3 - Applications

Controlling Input in the Tutorial

Submitted by Smbat on Wed, 2020-07-29 22:41
Category: 
Scoring

Hi All,

I am trying tor learn Rosetta basics using the tutorial https://www.rosettacommons.org/demos/latest/tutorials/input_and_output/input_and_output 

However, when I try like it is instructed in the tutorial following error happens:

Infinity4s-iMac-2:main smbatgevorgyan$ cd demos/tutorials/input_and_output/

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Rosetta 3 - General

Calling SnugDock from PyRosetta

Submitted by shruthi.murali on Wed, 2020-07-29 15:10
Category: 
Docking
PyRosetta

I am very new to the PyRosetta platform and was hoping to get some guidance on how I can do a SnugDock run from the PyRosetta interface with an antibody pdb and antigen pdb, as I know that the ROSIE queue can be quite long. I've seen the PyRosetta 4.0 documentation for SnugDock but am a little bit overwhelmed as I'm not too well versed in Python. Any level of guidance would be greatly appreciated! 

 

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PyRosetta - General

Zero residues error in docking

Submitted by cjy318 on Tue, 2020-07-28 19:47
Category: 
Docking

Hello, I need some help.

I have no residues error during my docking process. But refining and cleaning worked well with my PDB file.

Also, 1 year ago, docking process worked well with same PDB file and older version of rosetta.

I don't know why it happened.

My PDB file is attatched. please help me.

 

It is my rosetta crash log.

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Rosetta 3 - Applications

RosettaAntibody3 core.pose.util error

Submitted by linhhoang157 on Tue, 2020-07-28 12:40
Category: 
Structure prediction

I'm using rosetta_src_2020.08.61146_bundle. I'm trying to use the RosettaAntibody3 workflow as documented here, but am running into the following error when I run the following command: 

module load rosetta/2020.08 blast/2.10.0+ gcc/9.1.0
antibody.default.linuxgccrelease -ignore_unrecognized_res true -fasta IL6antibody.fasta -out:path:all antibodied

Here is the IL6antibody.fasta file:

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Rosetta 3 - Applications

getting right protonation state from PKa of Rosie

Submitted by hajar on Fri, 2020-07-24 16:24
Category: 
ROSIE

Hello,

Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?

Also, there are two options in pKa program in ROSEI:

1.Pack side chains and protonation states of the residues neighboring the target residue during pKa calculations

2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pKa calculations

 

which one should  we use to get the right protonation state?

 

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ROSIE - General

clean_pdb not working

Submitted by Andre Serobian on Thu, 2020-07-23 04:48
Category: 
Compilation

The simple clean_pdb.py does not function.

When I look at the script it is trying to print the wget_cmd command, WHY??

Here is the input and output:

python /home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py 2n2a AB
  File "/home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py", line 56
    print wget_cmd
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(wget_cmd)?

What is wrong here?

 

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Rosetta 3 - Applications

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