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Clustering and Protein Preparation for docking

Submitted by MRH on Sun, 2013-08-25 22:01

Hi everyone,
1)I have some doubts on clustering. I have modeled a protein and refined its loop. How exactly clustering will help me in further steps? and whats going to be the output result which i can use later? and do i need to use relax_a_large_protein option to the final model? (my protein contains 290 amino acid) or directly use the final model for docking studies?

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Rosetta 3 - General

run unit test error

Submitted by PoonamPandey on Sat, 2013-08-24 13:06

python test/run.py -d /rosetta3.2/rosetta_database --mode=release UnitTestExecutable = ["protocols.test", "core.test", "ObjexxFCL.test", "numeric.test", "utility.test", "apps.test", "devel.test"] --mute=MUTE-all
I got following error:
....
Paths: cd build/test/release/linux/3.5/32/x86/gcc/ && command line: ./apps.test --database /rosetta3.2/rosetta_database -mute MUTE-all
Running 1 test
Test suite: LigandDockTest (test/apps/public/ligand_docking/ligand_dock.cxxtest.hh)
core.init: Mini-Rosetta version exported from unknown

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Rosetta 3 - Build/Install

loop modeling

Submitted by MRH on Thu, 2013-08-22 23:19

Hi everyone, i am getting errors in loop modeling, this might be very basic, but i could not able to understand these.

1) remove_loop_coords.py is showing some error, like

line 23, in set_loop_from_string
self.start = int(loop_array[1])
IndexError: list index out of range

I have only one loop in loop file.

2) when i run loopmodel.linuxgccrelease for each line it says

ERROR: Illegal value for integer option -loops:frag_sizes specified: 1
ERROR: Illegal value specified for option -loops:refine
ERROR: Illegal value specified for option -loops:remodel : quick_ccd
etc..

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Rosetta 3 - General

minimum number of nstruct to build at 65% homolgy

Submitted by MRH on Thu, 2013-08-22 07:29

Hi everyone, I am trying to model one protein using template which is ~65% homologue, i used comparative modeling protocol given along with the software, my question is how many "nstructures" we have to make , what is the standard number, i used 1000 but it seemed never ending in my lap top, so i stopped that, what is the minimum number of nstructures i can apply? and after getting structure what other applications i have to use in-order to make it final?

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Rosetta 3 - General

Comparative modeling

Submitted by MRH on Mon, 2013-08-19 23:08

Hi everyone, I am trying to model one protein using template which is ~65% homologue, i used comparative modeling protocol given along with the software, my question is how many "nstructures" we have to make , what is the standard number, i used 1000 but it seemed never ending in my lap top, so i stopped that, what is the minimum number of nstructures i can apply? and after getting structure what other applications i have to use in-order to make it final? i am very new for Rosetta, suggestions would be very helpful for me, thank you.

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Rosetta 3 - Applications

A problem with "molfile_to_params.py"

Submitted by Rosettasz on Mon, 2013-08-19 19:35

Hello everyone,

I was trying to use "mofile_to_params.py" to generate a parameter file for several ligands that are to be used in RosettaLigand, while there seemed to be kinda bugs.

I downloaded ".sdf" file of the ligands from PDB;
added hydrogens to the ligands in Pymol;
used "babel" to create a new ".sdf" file in which hydrogens were added to the ligands;
used "molefile_to_params.py" and the new ".sdf" file to create a parameter file as well as the ligand conformer libraries.

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Rosetta 3 - Applications

Minimization of structure after each trial move in PackRotamersMover

Submitted by wymore-ornl on Fri, 2013-08-16 18:58

Hi,

I am still relatively new to PyRosetta so excuse my ignorance if the answer to this question is obvious.

I would like to do protein design calculations and the material I have read uses PackRotamersMover. I'm having no problems running these calculations. But I am not sure how to do some minor minimization of the structure after each design move when I apply PackRotamersMover. So when the algorithm outputs at the end that it built X rotamers at Y positions, I would like for it to have done X minimizations too.

Any help with this matter is much appreciated.

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PyRosetta - Scripts

Ligand atom RMSD calculation

Submitted by lkrathn on Wed, 2013-08-14 21:25

Hi Rosetta team,

I am trying to learn ligand docking using Rosetta. In my ligand docking trials, I have docked a different ligand in to a protein in which the original ligand was replaced. In this case both (original and new) ligands have similar core structure but they are different in substitution groups. Since core atoms and core structure of both ligands are similar, is there a way to calculate RMSD for ligand core atoms?

Thanks in advance.

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