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loopmodel mpi build fail

Submitted by Nicky_Learning_... on Mon, 2015-05-04 07:48
Category: 
Compilation

Dear Rosetta Developers

I'm quite new to Rosetta. Recently, I want to perform a loop modeling using Rosetta. So I want to compile Rosetta-3.5 on our cluster.
[root@c02125 ~]# cat /proc/version
Linux version 2.6.32-220.el6.x86_64 (mockbuild@c6b18n3.bsys.dev.centos.org) (gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC) ) #1 SMP Tue Dec 6 19:48:22 GMT 2011

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Rosetta 3 - Build/Install

Minimization Issue: Coarse Graining to All atom modeling

Submitted by abolia on Tue, 2015-04-28 10:52
Category: 
Docking
Design
Loop Modeling

Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.

Thank you.

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Rosetta 3 - General

Pepspec options

Submitted by shaunmk on Mon, 2015-04-27 02:33
Category: 
Design

Hi,

I'm using pepspec to design a peptide. I've been able to run the application with some options (listed below) but my peptides always seem to fly off into space, with the exception of the region near the anchor residue. I've tried a few different combinations by looking at the application documentation, but I can't seem to get anything that looks "reasonable". My options are:

-pepspec::soft_wts soft_rep.wts

-pepspec::interface_cutoff 5
-pepspec::clash_cutoff 5.0

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Rosetta 3 - Applications

Rosetta dock irmsd

Submitted by Pernille on Sun, 2015-04-26 13:51
Category: 
Docking

Hi Rosetta people

I have an odd problem concerning the interface rmsd output from rosetta dock.
I have two structure outputs from different runs. Only difference is using saxs as restrain in one run otherwise the scripts are identical.
I get better irmsd from the saxs run (0.333 vs. 1.116) but when looking at the structures there is barely any difference, I have checked rotamers as well.

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Rosetta 3 - Applications

Output format

Submitted by Michele Tavanti on Sat, 2015-04-25 05:03
Category: 
Docking

Hi everyone,

I am trying to carry out some docking experiments: I have the structure of my protein in .PDB and then the cofactor NADP in .sdf.
I think that I have some problem with the output: I can only open the structure of the protein and then the .sdf of the cofactor which is not docked.

The main thing you need to know is that I am not an expert at all in this field, and I would be grateful if someone could help me to carry out the docking and visualizing it. Currently, I am using Pymol to visualize structures.

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ROSIE - General

JobDistributor problem in antibody modeling

Submitted by Wizard on Wed, 2015-04-22 00:35
Category: 
Structure prediction

Hello everyone,

I build Rosetta 2015.12 on Scientific Linux 7 (SL-7). And, I follow the protocol of RosettaAntibody3 to do antibody modeling. 

(https://www.rosettacommons.org/docs/latest/antibody-protocol.html)

When, I run the script of “antibody.py” through following command as

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Rosetta 3 - Applications

Rosie Server Docking2, wrong plots output?

Submitted by Conan on Tue, 2015-04-21 12:18
Category: 
Docking

Dear All,

Any one knows why the Rosie Server for protein docking (docking2) automatically gave two plots that seem not consistent with each other on the x-axis which is the "RMSD". Or me please give some suggestion if I understand something wrong. Please see the attached figure.

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ROSIE - General

Error while reading in silent file

Submitted by rweisse on Mon, 2015-04-20 00:31
Category: 
Docking

Hi all, I am facing an error, when reading in the silent output file after a docking simulation. Here I used 6 cores to create 2000 decoys each (sum 12000). See the flag file attached. I used a slightely modified version of the ligand docking application, which is provided in the ROSETTA examples.

Now, i tried to combine all six output files to compare the results. Actually, I tried it with the following command

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Rosetta 3 - Applications

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