setup_RosettaCM.py
Submitted by browns02 on Mon, 2021-06-28 07:13
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Structure prediction
How to provide multiple templates for Robetta with RosettaCM option?
Submitted by lanselibai on Wed, 2021-06-23 14:06
Category:
Structure prediction
The FAQ of robetta said "You can load multiple templates, modify the alignments, add constraints, and more before submitting.“ However, I cannot find the option for loading multiple templates on the Robetta webserver. Is that possible?
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RosettaCM: threading okay, but hybridize loses many secondary structure
Submitted by lanselibai on Wed, 2021-06-23 13:51
Category:
Structure prediction
I use two templates to run the RosettaCM, each template representing different parts of the target. The threading step can retain most of the secondary structure. However, when doing the hybridize step, one part in the target loses half of its beta-sheets. Is this a common issue?
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RosettaCM: "Ligands must be added to all templates"
Submitted by lanselibai on Tue, 2021-06-22 10:42
Category:
Structure prediction
The RosettaCM requires Ligands must be added to all templates with a non-zero weight in the XML file!
In my case, the templates represent different parts of the target, so some template includes the ligand while some template does not. Do I really need to add the ligand to the template that does not have the ligand?
If it is necessary, how to do it? It is not likely to use some alignment to "estimate" the ligand location in the template.
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Add a ligand with only one atom (i.e. Zn) to the RosettaCM
Submitted by lanselibai on Tue, 2021-06-22 10:28
Category:
Structure prediction
My understanding for adding the ligand is to use the molfile_to_params script to generate XXX.cen.params, XXX.fa.params, XXX.tors files.
My ligand is just a one atom Zn. When molfile_to_params script is used, I got this error
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How to Perform point mutations with NCAA
Submitted by Subhrodeep Saha on Tue, 2021-06-22 02:05
Category:
Structure prediction
Hello Everyone,
I am trying to mutate multiple residues of a peptide with NCAA to determine their structure and ΔΔG of mutation on Rosetta.
I would be grateful if anyone could share any research article, material or guidance to proceed on this matter.
P.S. - I am a beginner at Rosetta without any bacl ground in coding or bioinformatics. Any help and advice is appreciated.
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Obtaining all PDB IDs containing similar binding sites for a specific ligand
Submitted by Antonia on Wed, 2021-06-16 12:30
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
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Internal error while running AbinitioRelax
Submitted by Subhrodeep Saha on Sun, 2021-06-13 03:44
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]
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Blast error for rosetta antibody: No argument value given for Query file
Submitted by dngusdnr1 on Tue, 2021-06-08 17:32
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
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Blast error for rosetta antibody: No argument value given for Query file
Submitted by dngusdnr1 on Tue, 2021-06-08 17:30
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
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