The problem has been solved
Anyone use unbuntu 16.04?
I installed gcc-6 , g++6, scons-2.51. all install correctly. as I checked -- version all correct.
option1, when I compile the Roseta source code ( Version 3.8)
$ ./scons.py -j 4 mode=release bin
The program runs long time. but at the last I got
usr/bin/ld: cannot find -lz
I'm trying to predict where a small molecule ligand will dock to a dimer protein and am trying to do a completely blind search. To do so, I use the start from mover to place the ligand at the center of my protein and then the initial perturb option in the Transform mover to randomly move it outside the protein. Since the protein is not circular, depending on which direction the ligand goes, it can end up pretty far from the protein. If this is wrong, or there is a better way to do it, feel free to let me know.
Hey,
So I ran a docking simulation in which I docked a small molecule to a dimer metal containing protein. I generated 1000 structures output into a silent file. I wanted the top 10 scoring structures just to see if the run worked and used "grep '^SCORE' IPDock/IPDock.out > IPDock/IPDockScores" to extract scores, the sort command to order them and created a file with the top ten structures.
Dear All,
Is there a URL or FTP to download the vall.jul19.2011.gz database?
I know the database resides in {ROSETTA}//tools/fragment_tools/
But if I want to direct someone to just download the database without downloading Rosetta and uncompressing it (for example to use PyRosetta independently than Rosetta). Does a URL or FTP to download the database exists?
Dear All,
Is there a tutorial that can show how to preform fragment picking in PyRosetta? I want to generate fragments for many structures and I do not want to overwhelm the Robetta server, thus I want to preform it in-house.
Any help on how or where to start to generate fragments using PyRosetta? I found that there is a mover FragmentPicker() in pyrosetta.rosetta.protocols.frag_picker but I do not know how to use it.
This is my code so far:
Dear All,
I am following the PyRosetta tutorial to learn how to preform global docking.
I wrote the following script:
Hi everybody!
I'm trying to learn how to use Rosetta in de novo protein design. I use this article as a manual: https://www.ncbi.nlm.nih.gov/pubmed/23744289
It doesn't work for me at some point. Namely, when I go to step 13 (Running the comparative modeling job), I try to execute the following command in the terminal:
./loopmodel.default.linuxgccrelease @modeling.options -database rosetta_database -nstruct 100
But the response is:
Hi,
I am trying to dock a small molecule with holo dimer protein (153 aa, 1 Cu and 1 Zn per chain). I followed the Ligand Docking Tutorial and it all works fine until I try to generate more than ~50 output structures. Using both MPI and default builds, all 8 GB of RAM and 5 GB of Swap are slowly filled up until my linux system kills the program. Below I have listed different commands and how many strucures it generated before swamping memory. The basic options file and xml file is attached is attached.
Dear All,
I am learning how to do protein-ligand docking and I am following the Rosetta built-in tutorial: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial
I did not change anything whatsoever. I used the same tutorial files (as is) and attempted to run the calculation as such:
{PATH_TO_ROSETTA}/main/source/bin/rosetta_scripts.linuxgccrelease @options
Hi,
I have a function in pyrosetta that performs repack, and I call this function many times. Right now I get tracer output from core.pack.task:
e.g.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 143 rotamers at 8 positions.
Is there a way to mute this output ONLY while in my function? i.e. I'd like to mute this output and then turn it back on later in my script?