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hydroxyproline patching problem

Submitted by aaj on Mon, 2016-02-22 07:33
Category: 
Chemically Modified Residues

Hello All

My docking_prepack application is incorrectly patching the hydroxyproline residues. Although the log file indicates that the full-atom patch is correctly read from the fa_standard/patches and also successfully patched, the output prepacked file contains a bond between the CD as well as CG to the OD1 of the HYP residue.

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Rosetta 3 - General

Space Swap!!!

Submitted by jrcf on Sun, 2016-02-14 11:43
Category: 
Structure prediction

Hello people.


it is normal for cluster.py occupy much space in the swap? I am following this tutorial, I had problems occupy the entire swap, and the program stops running, it increased to 54Gb, and still is using almost entirely.
It is running for more than 22 hours, and apparently will take all of the memory again and crash the program.

the script is:

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Rosetta 3 - Applications

Error_fragment_generation

Submitted by Payal Chatterjee on Fri, 2016-02-12 12:11
Category: 
Fragment Generation

Hi

I was running makefragments.pl for my short length peptide (sequence length 6), as a pre-requirement for abinito FlexPepDock, and I am getting the error:

Error: expected creation of t001_.200.9mers after running  "/path/to/make_fragments.pl/fragment_picker.static.linuxgccrelease @t001__picker_cmd_size9.txt -j 1'!

It was working fine before, but with two abnormalities:

a. It was generating only 3 and 9 mers(no 5 mer): so I corrected the make_fragments.pl, where in "my @fragsizes" definition "5" was missing.

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Rosetta 3 - General

Missing CS-HM-Rosetta Binary files

Submitted by Marius1987 on Wed, 2016-02-10 05:52
Category: 
Structure prediction

Dear All,

I try to determine protein structures using CS-HM-Rosetta.

It is stated in the supporting information (http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1202485109/-/DCSupplem...) that we need  execution of "cm_scripts/bin/predict_distances.pl sequence.fasta sequence.aln –aln_format grishin –outfile sequence.dist_csts" in order to generate the homology constraints.

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Rosetta 3 - Applications

Antibody Modeling Question

Submitted by rbehan on Fri, 2016-02-05 13:57
Category: 
Structure prediction

I'm trying to model a structure of an antibody.  I have an initial starting structure, which I have generated using a separate online server, and I have prepared the structure for modeling with rosetta.  I've been using the application "antibody_model_CDR_H3" which simultaneously docks Vh-Vl and samples loop conformations for HCDR3.  

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Rosetta 3 - General

docking mover(s) in rosetta

Submitted by aaj on Mon, 2016-01-25 02:38
Category: 
Docking

Hello all

What is the difference between the DockingMover and the DockingProtocolMover? From what I could gather on the rosettascripts webpage, dockingmover allows design while the protocol has no option for design. But is the difference limited to this. Also what does it mean by "post refactoring" docking protocol.

Thanks

aaj

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Rosetta 3 - General

Error message: ArchiveManager spinning down

Submitted by Lati on Sun, 2016-01-24 02:42
Category: 
Structure prediction

Hi Rosetta community! 

The first run I created worked perfectly, but for some reason creating another run for the trimed sequence is not working! I got this error message after about 1min of starting the run: 

ERROR: error detected in ArchiveManager -- spinning down

ERROR:: Exit from: src/protocols/jd2/archive/ArchiveManager.cc line: 426

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD 

with errorcode 911.

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Rosetta 3 - General

Adding included libries to scons

Submitted by Al52 on Wed, 2016-01-20 16:10
Category: 
Compilation

Hello.

I am running a pilot app which uses a test class that requires the cxx test header. I was able to include the path to the compiler by using the -I parameter. However when I try to use scons to build the pilot app executable I don't know how to get scons to add in the extra -I parameter.

Thank you.

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Rosetta 3 - Build/Install

Intel Compiler - Inaccurate G! step errors

Submitted by dtrudg on Tue, 2016-01-19 07:33
Category: 
Compilation

Hi,

We are trying to get Rosetta setup fo a user here at UT Southwestern, and have downloaded and built the 2015.39 release using the Intel Composer XE 2015 compiler suite, with MVAPICH2 2.1 as the MPI stack. This is the standard compiler/mpi stack we use for a large amount of other software on the cluster. Compilation of Rosetta followed the site settings file distributed for the TACC stampede cluster.

When the user runs a simple test of relax.linuxiccrelease:

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Rosetta 3 - Build/Install

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