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Troubles using RigidBodyTransMover and RigidBodyPerturbMover

Submitted by alejandro on Thu, 2011-04-21 06:11

Goodmorning,

I'm currently experiencing some troubles while using the RigidBodyMovers and I hope someone could explain me this strange problem. I perform a rigid body move and calculates its energy. But the result is different if I evaluate the energy after having stored the pose in a .pdb. Here is the code.


// Creating the poses and the scoring function
core::pose::PoseOP pose = new core::pose::Pose();
core::scoring::ScoreFunctionOP score_fxn = core::scoring::ScoreFunctionFactory::create_score_function("standard");

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Rosetta 3 - General

Destination of score.fsc file

Submitted by anirbanzz on Wed, 2011-04-20 23:30

Hi,

I am running Abinitiorelax for protein structure prediction through submission script
. I find that every time I run it, the score file gets made by the name "score.fsc" in the home directory only.
How can I specify a name for this file and its output destination.

Thanks,

Anirban

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Rosetta 3 - Applications

ERROR: Option matching -s not found in command line top-level context

Submitted by xxx on Wed, 2011-04-20 05:38

The commandline is:
$/home/xxx/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease @flags -database /home/xxx/Rosetta3.1/rosetta_database/

The content of flags is:
-s /input/1brs.pdb (I also tried various formats and locations of directories for 1brs.pdb, none of them worked)
-dock_pert 3 8
-spin
-fake_native
#-dock_mcm
-mute core.util.prof ## dont show timing info
-out:overwrite
-out:file:fullatom
-out:file:o 1brs
-mute core.io.database

Before getting this error message in running rosetta, I had many troubles in the installation.

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Rosetta 3 - General

flexpep docking problem

Submitted by michael_luntan on Mon, 2011-04-18 17:15

Dear All:
I am very new to the peptide flexible docking. When I use the locally installed rosetta 3.2.1 to perform a peptide docking. I got the error as :

ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1369

The command line is :
FlexPepDocking.linuxgccrelease -database /usr/local/src/rosetta_database/ -s renum.pdb -flexpep_prepack > flex.log

I also attached the pdb file and log file.

Hope you can help me out! thank you so much!!

Best wishes,

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Rosetta 3 - Applications

problem when exact pdb from silent file

Submitted by wenchangyu2008 on Mon, 2011-04-18 00:42

Hi all,
I got a problem when I tried extracting pdb from silent file in the tutorial in Abinitio Modeling (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_...). Actually I got nothing when I tried that command to exact pdb out. And there is no error message coming out, which I thought is very strange.

Best,
Wenchang

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Rosetta 3 - Applications

Is it possible to do Abinitio folding from a linear structure.?

Submitted by monos_morpheus on Sat, 2011-04-16 09:13

Hi, I was thinking is it possible I generate a linear structure with AMBER and then use it in Abinitio module for de novo folding or I can generate a linear structure in Rosetta and use it.? Because from what I see, Abinitio only needs the fasta format and an input structure. So if my input structure is from PDB, then it doesn't make any sense to do de novo folding. In addition, how can I generate a fasta file with a certain protein seq i have in mind.? Thanks.

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Rosetta 3 - General

Dimer of dimers

Submitted by smiruthi on Fri, 2011-04-15 10:41

HI,

I want to use Fold and Dock on a small domain of a protein that forms a dimer-of-dimers. It is a 50 residue domain that is known to form helixes.

I am not able to get a reasonable quaternary structure for this protein using the below symm files. Any help would be deeply appreciated. Thanks!

D2.symm file:
...
set_dof BASEJUMP angle_x(0:360) angle_y(0:360) angle_z(0:360)
set_dof JUMP2 angle_z(0:90)

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Rosetta 3 - Applications

modeling residues with covalent ligand attachments

Submitted by sid on Fri, 2011-04-15 09:16

I'm working on modeling covalently modified residues in Rosetta/PyRosetta. These modifications are things like acyl intermediates or covalent inhibitors...basically small-molecule ligands covalently bound to protein atoms in the context of a polypeptide chain. While the algorithm was written to model covalent inhibitors for a particular drug target we're working on, I'm interested in expanding it to look at a larger set of covalently-bound protein-ligand complexes in the PDB (both self-docking, cross-docking, and apo-docking).

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Rosetta 3 - General

Is anyone using GCC and RedHat Enterprise 5 for Rosetta 3.2?

Submitted by smlewis on Thu, 2011-04-14 08:24

We are having an issue we can't troubleshoot:

src/numeric/HomogeneousTransform.hh: In member function 'numeric::xyzVector numeric::HomogeneousTransform::to_local_coordinate(const numeric::xyzVector&)':
src/numeric/HomogeneousTransform.hh:377: error: expected unqualified-id before '=' token
src/numeric/HomogeneousTransform.hh:378: error: expected primary-expression before '(' token
src/numeric/HomogeneousTransform.hh:379: error: expected primary-expression before 'static'
src/numeric/HomogeneousTransform.hh:380: error: expected primary-expression before 'static'

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Rosetta 3 - Build/Install

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