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ligand docking with rosetta_scripts.linuxgccrelease

Submitted by xpzhang on Thu, 2015-02-26 10:57
Category: 
Small Molecules

I installed the latest rosetta common (rosetta_src_2015.05.57576_bundle.tgz) and tried the following demo with error:
/demos/protocol_capture/2012/ligand_water_docking

setting ligand_soft_rep weight hack_elec to 0.42

ERROR: unrecognized score_type type hack_elec
ERROR:: Exit from: src/core/scoring/ScoreTypeManager.cc line: 477

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '1HXW_input_0001'
Error:

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Rosetta 3 - General

ddg_monomer: How the ddG is actually calculated based on the 50 trajectories? What scorefunction is used?

Submitted by lanselibai on Tue, 2015-02-24 02:38
Category: 
Structure prediction

(relevant files can be downloaded at https://copy.com/yOhxRslZzK8j9z0l)

Dear friends,
In the instructions about ddg_monomer,

https://www.rosettacommons.org/docs/latest/ddg-monomer.html

it is mentioned that "the most accurate ddG is taken as the difference between the mean of the top-3-scoring wild type structures and the top-3-scoring point-mutant structures".

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Rosetta 3 - Applications

Using "make_project.py all" omits "basic.dylib" from link binary with libraries in Xcode 6

Submitted by kmolloy717 on Sun, 2015-02-22 20:53
Category: 
Compilation

Hello.

Just switched to a new Macbook pro that came with Yosemite and Xcode 6. I downloaded rosetta_bin_mac_2015.02.57538_bundle.

While trying to run "make_project.py all", I had to copy the version.py into the "main/source/xcode" directory from the "main/source" directory.

Starting up Xcode and opening the project, some modules (like basic) compiled with no problems. However, when it tries to compile core.1 (and other targets), I get the following error:

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Rosetta 3 - Build/Install

Executing the clean_pdb.py script

Submitted by Rkfoury on Fri, 2015-02-20 10:16
Category: 
Docking

Hello All,

I am currently running RosettaCommons on linux and am attempting to run the clean_pdb.py script on my native protein.
As of now, I have changed it to an executable file as recommended, but I am unsure what the command is to run this script on a certain pdb.

As of now my command is $ python clean_pdb.py script path/to/pdb, but this doesnt appear to be correct. Can anyone direct me on what the script requires for a command and exactly what to type in so it runs it on my vinculin.pdb protein.

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Rosetta 3 - Applications

cannot find -lcr Rosetta3.5 installation

Submitted by samuelrpita on Fri, 2015-02-20 08:17
Category: 
Compilation

Dear 'Rosettaers',
I'd tried to compile the Rosetta3.5 on my Server[1] and I couldn't. I tried to compile Rosetta using this command: scons bin mode=release -j 24 extras=mpi,static cxx_ver=4.6 cxx=gcc After a few minutes of compilation the error came and it is following:

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Rosetta 3 - Build/Install

pKa job submitting problem

Submitted by syoifczeri on Tue, 2015-02-17 21:41
Category: 
ROSIE

Hello

I tried to submit a job to calculate residue pKa in the protein (http://rosie.graylab.jhu.edu/pka/submit)
But...

after input PDB file I clicked "Submit" and stopped at "Submitting pKa job...".

Is that caused by my data error ?

or, Is there a pKa application in the Rosseta 3.5 for standalone calculation?

Thanks for your help

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ROSIE - General

problem creating lips4 file using run_lips.pl

Submitted by adva on Sun, 2015-02-15 06:22
Category: 
Membrane

Hi,
I'm trying to generate the input files for membrane ab-initio. I already created the span file using OCTOPUS.
However, the run_lips.pl script keeps failing. It creates blast outputs (blast and blast.msa files) but the raw file is empty and the lips4 file contains only the header, and the lipo file is also without values.
I think there's some problem with the part running this script- "http://gila.bioengr.uic.edu/cgi-bin/lips/script.cgi".

Can anyone help me with that?

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Rosetta 3 - Applications

Access to latest CS-ROSETTA tools

Submitted by smg3d on Fri, 2015-02-13 13:57
Category: 
Compilation
Structure prediction
Fragment Generation

Have been trying to access the latest CS-ROSETTA tools without success for several days. Looks like www.csrosetta.org has been down for a while.

Any alternative to www.csrosetta.org to access latest cs-rosetta tools?

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Rosetta 3 - Build/Install

ligand flexibility

Submitted by dave on Thu, 2015-02-12 08:48
Category: 
Enzyme Design

Hi everyone,

I see some strange behavior of enzyme design with ligand.
1) I have created a library of rotamers, set path to this library in params file (by PDB_ROTAMERS rotlib.pdb) and run enzyme design. But there is still only translation and rotation of rigid body in the active site and no using of the rotamer library. Only when I start with ligand structure with some clashes in the protein pdb file I can see optimization of of torsion angles of the ligand. Can you please explain how it works?

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Rosetta 3 - General

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