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

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Rosetta 3 - Build/Install

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

Category:

Docking

Hello,

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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

Category:

Structure prediction

Hello,

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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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PyRosetta - General

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

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).

Using pyrosetta to generate quaternary structure of protein

minimize_with_cst and convert_to_cst_file for ddG_monomer issues/confusion

FASTA for Octopus

Compilation problems

BuildPeptide - Using Phosphorylated and Sulfated Tyrosine

Docking-I_sc values do not correlate

Docking-RMS value nan

Homology Modeling-no PDB output

Generating Atom Pair Constraints

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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).

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