The problem hasn't been solved
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
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.
Hello all,
To perform the Flex-pep-docking protocol (ab-initio mode), I need to create fragment files for the target peptide (with 8 residues). I have tried to do this with the make-fragment.pl script . However, I get the attached error. I have already installed the last version of Blast tools. please let me know what is the problem and how it can be solved?
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:
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
Hello,
I am trying to obtain the score produced during the 3D RNA-protein complex modeling process (I do not want to run the scoring function after).
https://new.rosettacommons.org/docs/latest/application_documentation/rna/rnp-modeling
I'm running a python script with minmover function. After pressing Ctrl + C， the program dies in about 30 seconds. I don't know why it takes so long. Is there a way to kill the job immediately ?
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
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
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.