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PackRotamersMover in another way

Category: 
Design

I want to design peptides, allowing redesign and side-chain packing, but no backbone changes. So far I'm using PackRotamersMover, but I would like to write my packer with fixbb instead to have more control.

 

My question basically is: why do the two following snippets of code not do the same? And what have I missed about PackRotamersMover in my version?

code 1:

Post Situation: 

RAbD with N-term,Proline-like ncaa returns segmentation fault during CCDEndsGraftMover

Category: 
Design
Chemically Modified Residues
Fragment Generation

Recently I'm stumbling with rosetta RAbD application (version 2020.08.61146) in hope to modify an antibody whose antigen containing a non-canonical,N-term, and PRO-like aa ,namely the pyroglutamic acid in its epitope. 

I generated params file according tutorials in :https://new.rosettacommons.org/demos/latest/public/design_with_ncaa/README,with input mol file below.

Post Situation: 

Pose is full atom and mover expects centroid, how do I handle it the best?

Category: 
Small Molecules

I'm trying to use pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader for a project of side-chain packing small peptides with a fixed backbone. I've gotten as far as building the Mover: instantiate the mover, giving it rebuild info and the string with selected rotamers.

The problem I run into comes when I try to apply it to the starting pose; I get a warning:

Post Situation: 

Relax in membrane pull my protein out of the membrane

Category: 
Membrane

Good day, 

I am having issues with the mp_relax protocol. I am testing the protocol directly from a PDB crystal structure, and the relax algorithm takes this structure out from the membrane region (as defined by the MEM residue). I am first optimizing the membrane location with the mp_transform (with the -mp:transform:optimize_embedding true option), which positions the protein in the membrane as expected. Then, the relax protocol pulls out the protein from this "correct" membrane position, leaving the protein completely exposed to solvent.

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ddG_RNA final energy different when modeling WT sequence

Category: 
ROSIE

Hi, I have been using the ddG_RNA tool within ROSIE to calculate relative affinities for my protein and a list of mutant RNAs. Included in the text file list is the WT sequence that is also specified in the PDB file. Based on how I understand the tool works, the ddG bind score for this RNA should be 0, since the value is relative to the WT sequence. Instead I get a score of 3.36. Any idea on why this would be happening? 

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Can anybody suggests some flags to run Rifdock?

Category: 
Design

Hello

I've tried to design some miniproteins, by following up "Baker lab 2020, science" paper. 

I want to use Rifgen in Rifdock to make disembodied amino acid contact.

But I don't know what flags to start.

 

They said the initial job of rifgen will take a long time.

On the Rifdock tutorial page, they said "to contact somebody doing some similar jobs and use their flag as a starting point"

So can somebody share your flags?

 

 

Post Situation: 

ligand dock into HEM containg pdb

Category: 
Docking

 Hi all

 I would like to dock  unknown chemical into PDB which have HEM as a cofactor

 But I want to fix the HEM molecule fixed during docking with constraint statement below

                 <RESIDUE_SELECTORS>
                        <ResidueName name="HEM" residue_names="HEM" residue_name3="HEM" />
                </RESIDUE_SELECTORS>
.

.

.

Post Situation: 

Scripts accompanying Hossenzadeh et al, 2001

Category: 
Design

Hi all,

I recently came across the paper titled "Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites" and wanted to try it out for myself. I downloaded the supplemental materials and tried to follow along the READMEs to test out Methods 1-4. But I am not able to actually get any of them to work even with the provided pdbs. Is anybody else having the same problem?

Here is what I have tried...

Post Situation: 

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