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Molecular oxygen

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

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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cyclization_type flag in simple_cycpep_predict

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

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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Problems with disulphide bonds during KIC

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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Error: Could not find scorefxns and name score12 in Datamap in rosetta_bin_linux_2017.39.59729_bundle

Category: 
Docking

Hi everyone,

I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:; 

 

 ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol  docking_stubs.xml

 

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Using ref2015 and talaris2014 in the same script

Category: 
PyRosetta

Hi,

I'm using pyrosetta compiled from rosetta_src_2017.39.  I was wondering whether it's possible to use both talaris2014 and ref2015 in the same script.  When I try to set up a scoring function using talaris2014 weights, I get this error:

pyrosetta.create_score_function("talaris2014")

ERROR: talaris2014(.wts) requested, but -corrections::restore_talaris_behavior not set to true. This leads to a garbage scorefunction.  Exiting.

 

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