The problem hasn't been solved
I am working on the Pyrosetta tutorial and I am trying to use protein fragments. Howevere there is a problem since the Robetta server keep on failing.
I am submitting this fasta file.
>poly_
AAAAAAAAAAAAAAAAAA
Is there anything wrong with my fasta format-
Knut J
how to do cluster after low resolution protein-protein docking? I follow the manually and use docking.sc file as cluster input file for clustering, but it doesn't work.
THX
Hi
I am using the docking_protocol.linux for high resolution complex. I found there are many parameters in *.fasc file such as:
fa_atr fa_dun fa_rep fa_sol hack_elec hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb interchain_contact interchain_env interchain_pair interchain_vdw.
So, I am wondering which one would be a measurement for final model selection?
BTW, could this protocol support MPI multiple CPU running?
THX
Hello:
I am wondering could restta consider the flexibility of backbone duirng protein docking?
THX
Hi everyone,
Does anyone know whether the packing option "packing::explicit_h2o" and "packing::solvate" work out in Rosetta3.1?
This paper "A 'Solvated Rotamer' Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces" said that Rosetta could recover water-mediated h-bond using a rotamer library called Solvated Rotamer. How to use it, add "explicit_h2o" or "solvate" flag ? But I read the code of Rosetta3.1 and couldn't find the source code implemented these two option.
Thanks!
Hi
I am thinking about starting to use Rosetta instead of ICM Pro. Are there any group in Scandinavia that uses Rosetta? Will there be an course that will be held in either Norway or Sweden for the use of either Pyrosseta or Rosetta 3.1?
Knut J
sorry,
i get one error message when i'm runing make_fragment. i don't know how to solve it. the show the message in the follow:
[blastpgp] WARING: a standard checkpoint file should have extension ".chk"
checkpoint psi-blast failed!
Dear all,
I am using rosetta for abintio calculations for a while now. I am curious to know what are other parameter other than mentioned in the documentation, to play with to simulate protein size of 150 aminoacids. I am not really satisfied with the results obtained with typical parameters and wondering my laptop took only like one hour to complete the job ( but heard previously it is computationally intensive process)
Here is my flag file
-database /home/vamsi/Programs/Rosetta31/rosetta_database/
-abinitio
-in:file:fasta inputs/t000_.fasta
Hi there,
Is it possible to use the relax app to relax an structure while restraining the C-alpha coordinates to their initial positions in order to stop things blowing up? There seems to be an option -constrain_relax_to_start_coords but it doesn't appear to have much effect when I tried using it.
thanks for your help!
What's the different between two rotamer library?
If I use dun08 instead of rosetta default library, can I get more accurate side-chain packing result?
