Using pyrosetta to generate quaternary structure of protein
Submitted by nasim.soltani58 on Thu, 2020-11-19 17:35
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minimize_with_cst and convert_to_cst_file for ddG_monomer issues/confusion
Submitted by Kharlamov1317a on Mon, 2020-09-21 08:46
Category:
Constraints
Generating Constraints File and Pre-Minimization Problems with ddG_Monomer Application -
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FASTA for Octopus
Submitted by Smbat on Wed, 2020-09-16 05:40
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Compilation problems
Submitted by Soler on Wed, 2020-09-09 13:30
Category:
Compilation
Hi. I have had some problems installing Rosetta 3.12, I have downloaded the source version, the zlib1g-dev package, gcc 9.3.0 and python 3.8.2, my operating system is Ubuntu 20.04.1 LTS. The problem is when I compile rosetta:
if I type: ./scons.py -j 2 mode = release bin ... this is the output from the terminal:
~ / rosetta / main / source $ ./scons.py -j 2 mode = release bin
if I type: ./scons.py -j 2 mode = release bin ... this is the output from the terminal:
~ / rosetta / main / source $ ./scons.py -j 2 mode = release bin
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BuildPeptide - Using Phosphorylated and Sulfated Tyrosine
Submitted by jlawrie on Thu, 2020-09-03 14:29
Category:
Chemically Modified Residues
Hello,
I am trying to build to both phosphorylated and sulfated tyrosine containing peptide squences to use for docking. Unfortunately, I am unable to use the BuildPeptide command to construct these peptides as aI always recieve a Segmentation Fault error. I would appreciate any help. I have been trying to convert the starting fasta sequences: GY[TYR:phosphorylated]EEIA and GY[TYR:sulfated]EEIA without any luck. I have been able to construct the unmodified peptide, GYEEIA, successfully.
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Docking-I_sc values do not correlate
Submitted by jlawrie on Wed, 2020-08-12 08:08
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Docking-RMS value nan
Submitted by jlawrie on Wed, 2020-08-12 07:03
Category:
Docking
Hello,
I am new to Rosetta3 and jsut trying to dock some generated ligands into a protein PDB. Based on the generated structures it appears the docking program is working well however, when I look at the score.sc file the rms vlaues for all the generated structures is nan. I do not really understand if I should be expecting rms values. I am docking a ligand into an unbound protein substrate. Any information would be helpful.
Justim
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Homology Modeling-no PDB output
Submitted by jlawrie on Wed, 2020-08-12 06:30
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Generating Atom Pair Constraints
Submitted by Peik on Wed, 2020-08-05 15:39
Category:
Scoring
Hi,
I'm trying to mutate and minimize a complex with atom pair constraints applied to the residues around the mutated position, but the constraints do not seem to be getting applied to my pose. This is what I have:
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Error when trying docking protocol with different ligand
Submitted by scyphs on Wed, 2020-08-05 04:37
Category:
Docking
Hi,
I'm coaching an iGEM team at the University of Warwick and they're doing some dock design to try to switch the specificity of a transcription factor to a different ligand. We've been able to run the docking protocol with the protein and it's native ligand and it is able to recapitualte the the native binding. However, when we try the docking protocol with the new ligand we run into this error:
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