You are here

Solved

The problem has been solved

Assesing the docking

Category: 
Docking

Hello,

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)

 

 

Post Situation: 

where is generate_ligens.linuxgccrelease?

Category: 
Small Molecules

Hello, everyone!

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?

Post Situation: 

How do you combine two .pdb protein structure files of the same protein?

Category: 
Docking

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).

Post Situation: 

Compilation problems

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
Post Situation: 

BuildPeptide - Using Phosphorylated and Sulfated Tyrosine

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.

Post Situation: 

Pages

Subscribe to RSS - Solved