The problem has been solved
Hello everyone,
I am trying to relax a structure while also applying constraints on spesific locations in order to force these locations to be a spesific distance appart.
so far my code is as follows:
Hello People,
I am not sure if this is the correct forum to ask this question, but I thought many people here would have knowlege to answer me.
Hi everyone,
I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:;
~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol docking_stubs.xml
Hi,
I'm using pyrosetta compiled from rosetta_src_2017.39. I was wondering whether it's possible to use both talaris2014 and ref2015 in the same script. When I try to set up a scoring function using talaris2014 weights, I get this error:
pyrosetta.create_score_function("talaris2014")
ERROR: talaris2014(.wts) requested, but -corrections::restore_talaris_behavior not set to true. This leads to a garbage scorefunction. Exiting.
I'm trying to run abinitio to predict the structure of a mutant protein homologue. using thwe following command line options:
AbinitioRelax.macosclangrelease -in:file:native ./input_files/input.pdb -in:file:fasta ./input_files/ACSM3.txt -in:file:frag3 ./input_files/aat000_03_05.200_v1_3 -in:file:frag9 ./input_files/aat000_09_05.200_v1_3 -database $ROSETTA3_DB -nstruct 1 -out:path ./output_files/ -out:pdb -abinitio::increase_cycles 10 -abinitio:rg_reweight 0.5 -abinitio:rsd_wt_helix 0.5 -abinitio:rsd_wt_loop 0.5
Hi,
I'm trying to use the InterfaceSasaFilter class and am running into an error. Any idea how to get around this issue? A snippet of the code is attached, along with the error message
-----------------------
> sasaFilt = pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter()
> sasaFilt.apply(pose)
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.
