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Structure prediction

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: 

Internal error while running AbinitioRelax

Category: 
Structure prediction

I am trying to learn Rosetta without any background computer science or bioinformatics. I tried to run the AbinitioRelax.default.linuxrelease program with the proper input files and got the following internal error -

[FILE]: src/core/chemical/GlobalResidueTypeSet.cc
[LINE]: 149
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to open file: /home/rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt


[END_MESSAGE]
[END_CRASH_REPORT]
 

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: 

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.

 

 

 

Post Situation: 

FastRelax Refinement severe clashes

Category: 
Structure prediction

Dear Rosetta community,

I am working with Rosetta version 2020.08.61146. have run into an issue of massive clashes when refining a part of a ribosome structure using FastRelax. I have previously used Fast Relax extensivly as a preliminary refinement step and its usually works wonders. This has been on individual chains and now I want to try to relax an entire subunit however Fast Relax seems to tear a few nucleotides apart. I attached images pre and post FastRelax as well as my RosettaScripts XML and shell output. 

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: 

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: 

RosettaCM/hybridize

Category: 
Structure prediction

Has anyone had trouble with the Hybridize mover in RosettaScripts in the lastest weekly release Rosetta 2021.16 (Release date: Friday, April 23, 2021)? My script that works with older releases has stopped working and seg faults in Stage 4. Other movers, for example FastRelax, work.

Any help is much appreciated! Thanks.

Post Situation: 

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