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Dear Rosetta Community,
I have been frequently and successfully using the mpi installed version of rosetta_scripts on my institute high performance computing cluster for the past couple of years. However, I have been running into parallelisation issues of late. The command I use to submit jobs on our cluster using PBS is as follows:
I'm trying to calculate the common heavy atom RMSD between a polypeptide fragment and a variant, but in reading through the various RMSD functions in pyrosetta.rosetta.core.scoring it isn't clear why all_atom RMSD functions don't fail when given two poses which differ by amino acid identity - can anybody explain what's going on under the hood here or direct me to some documentation that details it? Also, do/how can any of the protein RMSD functions specify heavy atoms only as a predicate?
Thanks, I'd appreciate any assistance.
Hello, I have been reviewing the docking movers to perform both types, global and local. I have been testing them for a while now and with the active options to perform the global docking first, very little movement and exploration of the protein is observed in the output, the disturbances are practically local instead of global, this occurs both for DockingProtocol Mover and for Docking Mover. Would I have to first use DockingInitialPerturbation Mover or else use global docking flags and then use DockingProtocol or Docking for local?
Hello, I would like to use or be able to visualize in the score file some terms or information related to docking and similar protocols, for example, interface_score and rms in other scoring functions executing other movers. Can this be done with flags? I hope you can help me, thanks.
I'm currently in conversation with my PI to get a PC mainly for protein modeling and MD simulations.
One of the software for protein modeling I want to use is rosetta, but unfortunately, I don't know what component I should focus on. RAM/CPU/GPU? all three of them?
I hope someone can help me.
Thanks in advance.
ps- I don't have a specific budget yet, so feel free to suggest to me the best configuration you can think of.
I have recently started using Rosetta and I wanted to generate the 3-mer and 9-mer fragments for Abinitio (without using the Robetta server).
I used the make_fragment.pl files provided under the fragment_tools folder in Rosetta to generate the files (by giving just the fasta file as an input). However, the result that I gathered was not the same, as what is generated by the Robetta server.
Dear Rosetta Users,
I'm new to Rosetta and fall into some errors when tried to test the installation.
I downloaded version 3.13 for Linux system. Then I did the installation according to the tutorial:
I extracted the binary
tar -xvzf rosetta_bin_linux_3.13_bundle.tgz
Since I have 12 cores I did and wanted to have MPI version of Rosetta
./scons.py -j 12 mode=release bin extras=mpi
The installation went smooth and I haven't got any error messages.