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NCAA attached at two points

Category: 
Non-Canonical Peptides

Hello,

I am trying to parameterize an NCAA which is a result of cyclization of the backbone, rather than just a PTM of an R group. I am using the molfile_to_params_polymer.py script (BTW is there a python 3 version of this script?) 

The connection points are at the R group of one residue, though there is a break in the chain (C=O -> C-OH) then a connection point to the nitrogen backbone atom of the subsequent residue.

When I use fixbb to modify to this residue I am getting the error:

Post Situation: 

Obtaining all PDB IDs containing similar binding sites for a specific ligand

Category: 
Structure prediction

Hi all, 

Is it possible to search the proteins having similar binding sites for a specific ligand in Rosetta? I need to classify proteins based their binding site similarities -in terms of RMSD. If it is possible, how can I do this? Thanks in advance. 

 

Antonia

 
Post Situation: 

Blast error for rosetta antibody: No argument value given for Query file

Category: 
Structure prediction

Hi there,

 When I try to run rosetta antibody with,

"antibody.linuxgccrelease -fasta mAb2.fasta | tee grafting.log"

I encounter error message " ERROR: basic.execute encounter error while runnning blastp [-db, /home/user/rosetta/rosetta3.13/main/database/additional_protocol_data/antibody//blast_database/database.FRH, -query, grafting/frh.fasta, -out, grafting/frh.align, -word_size, 2, -outfmt, 7, -max_target_seqs, 1024, -evalue, 0.00001, -matrix, BLOSUM62]

 How can I solve it?

Thanks

Post Situation: 

Blast error for rosetta antibody: No argument value given for Query file

Category: 
Structure prediction

Hi there,

 When I try to run rosetta antibody with,

"antibody.linuxgccrelease -fasta mAb2.fasta | tee grafting.log"

I encounter error message " ERROR: basic.execute encounter error while runnning blastp [-db, /home/user/rosetta/rosetta3.13/main/database/additional_protocol_data/antibody//blast_database/database.FRH, -query, grafting/frh.fasta, -out, grafting/frh.align, -word_size, 2, -outfmt, 7, -max_target_seqs, 1024, -evalue, 0.00001, -matrix, BLOSUM62]

 How can I solve it?

Thanks

Post Situation: 

adding NCAA to the N-terminal of RCSB pdb

Category: 
Non-Canonical Peptides

Hello,

I usually use my NCAAs by mutation in the sequences. 

Now, I am looking for a way or application in Rosetta to add, not mutation, NCAAs to the N- terminal and C- terminal of the sequences. 

The RCSB pdb starts with leu at N- terminal in attached picture that we need to add pyroglutamate before that 

 I wonder if anyone could let me know how I can add pyroglutamate using params file and rotlib file to the sequence. 

Post Situation: 

covalent ligand docking in Rosetta

Category: 
Docking

Hello,

I am modeling an enzyme and a substrate to study the enzyme specificity. From literature, I learned that the specificity is determined by the second step of the mechanism in which the ligand is covalently bound to D281 of an enzyme (see the attached picture showing the mechanism). Is Rosetta able to do covalent ligand docking? If so, how can I parameterize the ligand (which is covalently bound to the protein)? If not,  can I do covalent docking with other software(??) and then score it with Rosetta?

Post Situation: 

parameter file of GLU protonated (GLU_P1.params)

Category: 
Chemically Modified Residues

Hello,

I have a protonated GLU in the active site of an enzyme. I would like to use GLU_P1.params in my simulation by -extra_res_fa (the OE2 is protonated). I need to change the name of this protonated GLU in the PDB, but I am not sure what it should be. Because the NAME and IO_STRING are different and are not three letter code. Please see below and let me know what the name of this protonated GLU in the PDB file should be.

GLU_P1.params:

Post Situation: 

Segmentation fault on antibody structure prediction

Category: 
Structure prediction

On running antibody.macosclangrelease I was getting a segmentation fault. Now on switching to antibody.static.macosclangrelease I got the following error: SCS_BlastFilter_nonmatching_prolines::apply: Error! Could not cast SCS_Results to SCS_BlastResult

I was able to predict the structures for rest of my antibody models, I don't understand why this particular sequence is giving me a hard time.

 

 

 

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