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Post Situation: 

Disulfide Bonds in Loop Modeling

Category: 
Loop Modeling

Good Morning,

I was implementing the NGK loop modeling to fill the missing loops in the PDB structure, but the disulfide bonds in the PDB were broken and converted to regular cystines after the modeling. These disulfide bonds are not in the remodeled loop region and I specified '-loops:fix_natsc true'. From the output, it says: 

core.conformation.Conformation: Found disulfide between residues 76 166

core.conformation.Conformation: current variant for 76 CYS

core.conformation.Conformation: current variant for 166 CYS

Post Situation: 

Using NCAA

Category: 
Structure prediction

Hello,

I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation, I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31” it shows there is no parameters for C-N-C-CA

I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsion (i.e., importing 0 1 180.00 for related parameter in mm_torsion_params.txt)

 

Post Situation: 

Using NCAA

Category: 
Design

I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation , I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31”  it shows there is no parameters for C-N-C-CA

I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsions (i.e., importing 0      1 180.00 for related parameter in mm_torsion_params.txt)

 

Post Situation: 

hpatch commands and how to identify patches

Category: 
Scoring

Hi everyone!

I would like to determine the hpatch score for proteins to predict the affinity to lignin as described by "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity" by Sammond et al 2014 and developed hpatch by Jacak et al.

I tried to validate the method by BSA hpatch but it is not worked (the output was 8.0 whilw should be 36).

I also don't know how to obtain the hydrophobic patch area and how to identify it in protein structure.

Post Situation: 

Speeding up FastDesign

Category: 
Design
<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="r15" weights="ref2015.wts"/>
  </SCOREFXNS>
  <RESIDUE_SELECTORS>
    <True name="full_pose"/>
  </RESIDUE_SELECTORS>
  <TASKOPERATIONS>
    <ResfileCommandOperation name="rescmd" command="ALLAA EX 1 EX 2 EX_CUTOFF 1" residue_selector="full_pose"/>
  </TASKOPERATIONS>
  <MOVERS>
    <FastDesign name="design" scorefxn="r15" task_operations="rescmd" repeats="3">
Post Situation: 

trRosetta protocol Segmentation Fault

Category: 
Structure prediction

Hello,

So I've been trying to implement the new trRosetta protocol and I keep getting a segmentation fault error. Is there any idea what I might be doing incorrectly? The Rosetta Crash Log is below and is followed by the output logs (both raw text files are also included as attachments).

Post Situation: 

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