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How to read the output score file from rosetta?

Submitted by Sunyp_IM on Sun, 2017-08-27 05:29
Category: 
Compilation

Dear all, 

I find the score file output by rosetta is different to read. For example, a score-snugdock.sf file produced by snugdock reads like the following in gedit:

https://www.dropbox.com/s/6oba8nitiwob7pb/score.PNG?dl=0

I cannot tell the column names and their corresponding values. The Rosetta documnet gives a sort command that can pick out the structure with the lowest score:

 sort -nk5 score-snugdock.sf | head -n1 | awk '{print $NF}'

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Rosetta 3 - General

libmpc.so.2: cannot open shared object file

Submitted by ShaneHesprich on Fri, 2017-08-25 11:50
Category: 
Compilation

I am attempting to install Rosetta/3.8 on a Linux Cluster running Redhat 5.6. I am compiling with gcc/4.9.3 and mpich 3.2. I have come across the following error:

/exports/apps/gcc/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory

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Rosetta 3 - Build/Install

Relax is resulting in a Segmentation Fault

Submitted by brspurri on Thu, 2017-08-24 18:46
Category: 
Structure prediction

First off, I hate to be asking about a "Segmentation Fault" here because I know it can be any number of things; but I'm completely stuck and need to ask for help.

I am preparing a structure for downstream modeling, and I am running a very simple relax following the steps outlined here (the short protocol):

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Rosetta 3 - Applications

Allow region of protein to move in a certain direction

Submitted by sn on Wed, 2017-08-23 17:07
Category: 
Design

Hi,

I have a protein structure. I want to move a specified region (say residues x to y) of this protein in a any direction (more like a dynamic simulation). Is there a protocol that allows this in Rosetta? I have tried the backrub, relax with constraints.

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Rosetta 3 - Applications

Running snugdock was crashed by "segmentation fault"

Submitted by Sunyp_IM on Mon, 2017-08-21 05:03
Category: 
Compilation

Hello everyone,

When using the following command to run snugdock in my centos 7 system:

 snugdock.linuxgccrelease -s antibody_antigen_start.prepack_new.pdb \
     -ensemble1 antibody_ensemble.list \
    -ensemble2 antigen_ensemble.list \
    -detect_disulf false \
    -antibody:auto_generate_kink_constraint \
    -antibody:all_atom_mode_kink_constraint \
    -nstruct 20 \
   -multiple_processes_writing_to_one_directory > snugdock.log 2>&1 &

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Rosetta 3 - Applications

The problems on pdb renumbering

Submitted by Sunyp_IM on Sun, 2017-08-20 06:39
Category: 
Compilation

Hello everyone,

I am learning to do antibody-antigen docking with snugdock. The antigen I am working on has two chains (chain A and B). Before the antigen pdb file can be used for docking, it must be renumbered (changing it to a single A chain and numbering all residues continuously), am I right? There is some renumbering scripts in the Rosetta package. I have tried some of them, but none can work. 

(1)  The pdb_renumber.py script in the /app/rosetta_src_2017.08.59291_bundle/tools/protein_tools/scripts directory. The command:

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Rosetta 3 - Applications

Ligand params file proton_chi parameters

Submitted by staciekim on Thu, 2017-08-17 14:50
Category: 
Docking

Hi,

I am using RosettaLigand application to dock a small molecule into the active site of an apo-protein structure of my interest. Instead of using a pre-generated conformers, I am using the "dummy" method of specifying proton_chi sampling for all freely rotating bonds. (So even for C-C or C-O bonds, I would add another proton_chi line below to add sampling for those chi angles)

My question is simple, but it seems pretty hard to google anywhere to find documentation for the parameters following PROTON_CHI

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Rosetta 3 - Applications

Produces a set of rotamers from a given residue

Submitted by a-eatemadi@razi... on Tue, 2017-08-15 08:05
Category: 
Docking

Dear Rosettaers

I would like to dock Individual residues against the target surface on my protein. In this way, I have to produce a set of individual hydrophobic rotamers which can bind to a hydrophobic pocket on my protein. 

I used this RosettaScript to generate inverse rotamers:

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Rosetta 3 - General

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