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This is a continuation of an earlier thread, but I am still having trouble getting the surface_docking application to accept my inputs of a protein and ice surface. After correcting issues with hydrogen naming and now using the -ignore_waters false flag so that rosetta does not delete the ice surface, I am still getting the following error (this was all the error output):
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.
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.
(New user to Rosetta, so I apologize if this is the wrong place to post this or a silly question)
I am trying to use the Surface Docking application (https://www.rosettacommons.org/docs/latest/application_documentation/docking/surface-docking) to dock a protein to a crystal surface using only a fasta sequence file.
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.
I am using RosettaLigand application to dock a small molecule into the active site of an apo-protein structure of my interest. Instead of using a pre-generated conformers, I am using the "dummy" method of specifying proton_chi sampling for all freely rotating bonds. (So even for C-C or C-O bonds, I would add another proton_chi line below to add sampling for those chi angles)
My question is simple, but it seems pretty hard to google anywhere to find documentation for the parameters following PROTON_CHI