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cyclization_type flag in simple_cycpep_predict

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cyclization_type flag in simple_cycpep_predict
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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).

I tried to turn on or off some other flags (-cyclic_peptide:require_disulfides or -cyclic_peptide:cyclic_permutations) but it didn't change anything. My input file seems to be correctly read by the program (the peptide sequence of the output models is the one I expect), and the N- and C-term are both cysteins. But during the computation, the program applies constraints on N/CA atom of the first residue and CA/C atoms of the last residue.

 

Below is a typical output with a toy sequence:

protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Building sequence CYS ALA ALA ALA CYS.
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Build successful.
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond between residue 1, atom  N   and residue 5, atom  C  .
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up cyclic constraints.
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: The following four atoms define the terminal bond:
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 1.     Res=5   Atom= CA
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 2.     Res=5   Atom= C  
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 3.     Res=1   Atom= N  
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 4.     Res=1   Atom= CA
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Finished setting up constraints.
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Randomizing mainchain torsions.
core.kinematics.AtomTree: DOF for this torsion angle could not be found in AtomTree.
core.conformation.Conformation: Unable to set torsion angle in atom_tree: TorsionID 1 BB 1
core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 5-1, 5-2, 5-3, 1-1!
core.kinematics.AtomTree: DOF for this torsion angle could not be found in AtomTree.
core.conformation.Conformation: Unable to set torsion angle in atom_tree: TorsionID 5 BB 2
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Performing GeneralizedKIC closure of loop.
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond between residue 1, atom  N   and residue 5, atom  C  .
protocols.relax.FastRelax: ================== Using default script ==================
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.generalized_kinematic_closure.GeneralizedKIC: Closure unsuccessful.
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Closure failed.  Continuing to next job.

 


To note, I also had to modify slightly the file main/source/src/basic/options/options_rosetta.py prior to compiling as the routine simple_cycpep_predict routine used to complain (ERROR: Option matching -cyclic_peptide:cyclization_type not found in command line top-level context).

 

I'm using Rosetta 3.8, compiled with clang 5.0.1.

Any help appreciated!

 

Florent

Post Situation: 
Thu, 2018-01-04 09:22
Florent Langenfeld