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Error when run script "thread_pdb_from_alignment.py"

Submitted by carlos_andre on Fri, 2018-03-09 09:38
Category: 
Docking

Hello guys,

I'm using the ligand docking protocol, and when I put the command below it does not generate the expected output file "2ou0_threaded.pdb"

command:

/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py --template=2anv_A --target=2ou0_ --chain=A --align_format=clustal alignment.aln 2anv_A.pdb 2ou0_threaded.pdbD

Error:

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PyRosetta - Scripts

An issue with GenericMonteCarloMover()

Submitted by ac.research on Wed, 2018-03-07 13:57
Category: 
Design

Dear All,

I  have the following code that i wrote back in summer 2017 and it worked perfectly until February. But then I started to get strange errors (and I have not modified my code at all). After investigating it seems that the GenericMonteCarloMover() is deleting the content of the pose after the .apply(pose). In other words, after the mover is done i get an empty pose (no length and no sequence).

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PyRosetta - General

The algorithm of adding missing Hydrogen to a backbone

Submitted by ac.research on Tue, 2018-03-06 03:48
Category: 
Design

Hello people,

You know how when you import PDB structures into Rosetta and relax them Rosetta adds the missing hydrogens? What is the algorithm that does that?

I want to know the mathematical aproach, not the code; does it use rotation vectors and a rotation matrix to find the orientation and position the hydrogens? Does it use another approach?

I beleive this same algorithm is used to add/replace sidechain? it finds the orientation and angles of the side chains and replaces them?

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Rosetta 3 - General

Fix corrupted Backbone

Submitted by ac.research on Mon, 2018-03-05 12:48
Category: 
Design

Hello people,

I have a protein topology with a strange backbone (attached).

You can see that there is structure (several helices), but the backbone itself is not good enough to be able to do anything computationally with it, if ported into PyRosetta, PyRosetta it gets confused. So my question is how can I fix this backbone, nothing fancy just replace each position with Glycine or Valine or Alenine, but the proper ideal structure of the amino acid that will not result in clashed nor atoms occupying the same space?

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PyRosetta - General

Molecular oxygen

Submitted by matteoferla on Sat, 2018-02-24 06:05
Category: 
Small Molecules

I am planning on docking a ligand in a cavity with a heme and a constrained oxygen. Whereas I can make params of ligands and non-canonical residues, I cannot for molecular oxygen (OXY). It is not in the database either. Molfile_to_params.py gives the following 

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Rosetta 3 - General

test unit error cxxtestgen.py TabError: inconsistent use of tabs and spaces in indentation

Submitted by chemaniac on Thu, 2018-01-04 23:21
Category: 
Compilation

Hi,

I  sucessufully compiled release and debug libraries and excecutables. However,  when I get an error message for test units.  This is my log:

 

/scons.py mode=debug cat=test -j2

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Rosetta 3 - Build/Install

cyclization_type flag in simple_cycpep_predict

Submitted by Florent Langenfeld on Thu, 2018-01-04 09:22
Category: 
Structure prediction
Design
Constraints

Dear Rosetta users or developers,

 

I'm trying to model small, cyclic peptides with the simple_cycpep_predict routine. While I explicitely asked for a terminal disulfide cyclization (using the flag -cyclic_peptide:cyclization_type terminal_disulfide), the output models are cyclized with a mainchain bond (the default n_to_c_amide_bond).

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Rosetta 3 - Applications

error for the pose reading:TRP:NtermProteinFull:triazolamerC missing: C1

Submitted by wyb on Fri, 2017-12-01 17:50
Category: 
Design

Hi there,

I have a pdb file from CHARMM format. When I use

fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out

I got this:

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 A TRP TRP:NtermProteinFull:triazolamerC
core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CT1


and it skipped the first residue TRP.

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Rosetta 3 - General

Problems with disulphide bonds during KIC

Submitted by Loki01 on Tue, 2017-11-28 03:11
Category: 
Structure prediction

Hello.

I am new to Rosetta. I am trying to build a model of my protein but my disulphide bond seems to break after centroid stage (I am quessing here). The disulphide thats breaking is in the loop region I am trying to model. I have googled around and found some suggestions but nothing seems to work for me. Here are my flags:

 

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Rosetta 3 - General

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