The problem hasn't been solved
I didn't find the descriptions of these two options. Is there any documentations about it? What does -constraints:cst_fa_weight mean? Thanks~
I have finished the fragmentation step using CS-Rosetta (with file aa_t000.xx03xx.v_3 and aa_t000.xx09xx.v_3). Now I want to generate protein structures from them and meanwhile apply NOE distance constraints. I have tried to only build 1 structural model. The resulting pdb structure does not satisfy the NOE constraint. I have the following questions:
(1) what is the appropriate way to check the NOE distance constraints have been applied? In other words, is my expectation (the NOE constraint should be there even though only one model has been generated) right?
I use the low resolution protein docking these days. In one case,I use full atoms during protocol to generate 10000 poses and top 200 best score poses were clustered by cluster protocol. In another case, I just generate the 10000 pose with protein backbone and also cluster the top 200 best score poses. I found that the results between these two cases are different.
I am wondering which one should I use for the final protein docking solution?
Thank you very much
Hello:
I've generated one PDB file containing several strucrues of the same protein MD trjactory by VMD. I try to use the cluster protocol to cluster my structure, but it is always says: the PDB format can not recognize by Rosetta. I also split the one file into different indivisual structural files, but the error is still there.Could you please give me some advices for this issue?
Thank you very much.
Hi,
It seems that there is a bug in LoopMover_Refine_Backrub.cc. When I use this mover in my protocol, my programme exit with en error from BackrubMover::add_segment() function (input pose is null). So I read the code and found that the author may forget to set the input pose. I added two line codes after line 135 in LoopMover_Refine_Backrub.cc. Now it works.
line 134: protocols::moves::BackrubMover backrubmover;
line 135: backrubmover.branchopt().read_database();
/////////////////////my codes//////////////////////////////////
Hello:
I am wondering what's the general steps for Rosetta protein docking. I found there are two methods people usually use for protein docking by rosetta:
Method one:
low resolution docking(only backbone)-->cluster-->high resolution docking
Method two:
low resolution docking(only backbone)-->cluster--> relax (add sidechain with full atoms)-->high resolution docking
I am wondering which one is much more reliable?
Thank you very much
I have docked ligand in a receptor and now I want to perform a loop modeling. I tried using these flags:
-in::file::extra_res_fa aral.params
-loops::extra_res_fa aral.params
... but rosetta returns; ERROR: Option matching -in:extra_res_fa not found in command line top-level
Without these flags Rosetta returns:
ERROR: unrecognized aa ARE
(ARE is my ligand).
So, how do I get loopmodel to recognize my ligand?
Thanks,
Christoffer
How do you activate the domain prediction part of Rosetta, i.e. RosettaDOM?
Thanks,
Nasos
Hi
I used Fedora 14 with all updates. When I got the new version of sasa.cc it build okay until this points. I think there might be error in the optimalization either in Gcc or Rosetta. I have this email knutjorgen(at)gmail.com. Do you think I should open a bug in Fedoras bugdatabase,
gcc-4.5.1-4.fc14.x86_64
glibc-2.12.90-19.x86_64
gcc-c++-4.5.1-4.fc14.x86_64
I'm trying to install Rosetta on a Centos system using the comman in rosetta_source/readme.txt:
python external/scons-local/scons.py . I get the error message: ImportError: No module named os
Can someone please shed light on this for me?
Thanks!
Irene Newhouse
