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residue_energy_breakdown of a protein-ligand complex.

Submitted by sam_dc on Tue, 2021-05-18 04:45
Category: 
Docking

Dear Rosetta Users, 

I'm using the "residue_energy_breakdown" utility in order to obtain a per-residue energy breakdown of the residues that interact with the ligand in my protein-ligand complex generated by the RosettaLigand application.

In the POSE_ENERGIES_TABLE at the end of the docked model I read quite reasonable energy terms :

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Rosetta 3 - Applications

Issues with modifying dock.xml for multiple ligand docking

Submitted by DGR95 on Fri, 2021-05-14 12:51
Category: 
Docking

Hello all, 

I've been having some issues in modifying my dock.xml file for a multiple ligand docking run. I been trying to use the paper "RosettaLigand docking with flexible XML protocols" as a reference but no luck. According to the paper I should be trying to modify the <LIGAND_AREA> and <INTERFACE_BUILDER> taggs, but the paper only shows an xml file for a single ligand dock. I'm pretty new to this and rosetta scripts, so I'm not sure exactly how to proceed. Anyhelp would be appreciated. 

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Rosetta 3 - Applications

Rotate chain

Submitted by Germanico on Sun, 2021-05-09 16:36
Category: 
Design
 
I have a pdb with a homodimeric conformation for two alpha helix transmembrane domains.
This structure features a cross-like conformation, interacting at known residues.
I want to rotate each of the domains 15º along the z-axis
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Rosetta 3 - General

Disulfide Bonds in Loop Modeling

Submitted by code_Monkey on Mon, 2021-05-03 08:27
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

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Rosetta 3 - Applications

Using NCAA

Submitted by ate on Sat, 2021-05-01 02:52
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)

 

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Rosetta 3 - General

Using NCAA

Submitted by ate on Sat, 2021-05-01 02:22
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)

 

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Rosetta 3 - General

hpatch commands and how to identify patches

Submitted by Bianca Oliva on Thu, 2021-04-29 04:02
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.

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Rosetta 3 - Applications

Speeding up FastDesign

Submitted by ebetica0 on Wed, 2021-04-28 13:08
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">
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