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The problem has been solved
I followed the tutorial, and did docking. Now, I can see that the complex structure that I predicted is completely match the true complex structure. But, when I use TMalign and TMscore, they give me something like the following:
Name of Chain_1: predicted.pdb
Name of Chain_2: true.pdb
Length of Chain_1: 289 residues
Length of Chain_2: 579 residues
TM-score= 1.00000 (if normalized by length of Chain_1)
TM-score= 0.49914 (if normalized by length of Chain_2)
I am reading Mr. Baker's paper titled "Computational design of ligand-binding proteins with high affinity and selectivity". In the supplementary data, they used generate_ligens.linuxiccrelease to generate ligand conformers. But I can't find generate_ligens tool in my directory (~/rosetta/bin), also I didn't find any record about it in Rosetta tutorials. Anyone konws where to find it?
I have a *.pdb file of one protein. I need to do protein protein docking for this protein (I have the original one and I will also make a duplicate of it). What is the best way to combine the original one and the duplicated in one pdb file (I'm doing this to prepare the final pdb for docking).
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
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.