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Rosetta3.2 cluster application file-reading error

Hi, I was trying both Rosetta3.1 and Rosetta3.2 to do clustering. I had normal result from Rosetta3.1. But Rosetta3.2 failed to work. I used the same data set (generated by Rosetta2.3.0 abrelax mode), option and command, and the path is correct. I also got the error messege:

ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 80

And in the log file, it says:

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interpreting score values in silent output file after running abinitiorelax

Where can I find information that explains what the score values are and how to interpret and compare them? I'm new to Rosetta and still trying to learn what is going on while I learn how to run the program; so excuse me if I missed something obvious. Also, is the primary source of information related to Rosetta in published papers or is there something more explanatory than the Rosetta manual? Thanks for any help.

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Where is the flag -preserve_input_cb?

Hi, I need some help here. I've been reading the document for fixbb protocol in this page: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_...
In the box listing flags for rotamers, I found one called preserve_input_cb which is supposed to keep unidealized ca_cb bond parameters from input file. However, I cannot find which layers this flag belongs to. What's the key word should I put before the flag in the option file?

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Using 2 non-standard residues in one run

How do I identify two ligand residue type files? I'm docking two proteins, each with a prosthetic group that's near the docking interface. I've created the residue type files. I can only get it to recognize one of the two residues, whether I use -extra_res_fa [They're both in the same dir], or whether I use two -extra_res_fa statements, or if I string the full path & file names of both files after the -extra_res_fa statement.

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Docking 2 proteins including ligands

We'retrying to dock to heme-containing proteins together. The hemes are close to the docking interface, so we don't feel we should dock the proteins only. We've used molfile_to_params.py to create params files. When we try to dock, we get fold errors, as did a previous poster about 6-8 months ago. The recommendation was to try the flag -partners AB CD. When we do that, we get an error that docking:partners has multiple values & the job dies.

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cluster error

Hello:
I generated several conformation of my protein by CONCOORD and I try to cluster then with Rosetta. However, it doesn't work:

core.io.pdb.file_data: [ WARNING ] can't find atom for res 14 atom ND2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 14 atom OD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 15 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 15 atom CG2 (trying to set temp)

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Trouble building rosetta in windows with cygwin

I got this error message when trying to build rosetta 3.2 under windows XP in cygwin 1.7.8 using python 2.6.5.

scons: *** [build/src/release/cygwin/1.7/x86/gcc/utility.dll] Error 1
scons: building terminated because of errors.

Does anyone here know what might be causing this and how could get around this problem to get rosetta built? Let me know if you need more information.

Thanks.

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-score_app:linmin flag not working

Hi All,

I am completely new to this forum and to rosetta, so be kind with me...

I am trying to minimize a structure using rosetta and more specifically -score_app:linmin flag together with score_jd2.linuxgccrelease. First I don't have in my installation the score.linuxgccrelease executable, is that a mistake? Are score.linuxgccrelease and score_jd2.linuxgccrelease similar / identical /different?

Second I tried to run the following command, without much success :-(
>score_jd2.linuxgccrelease -database $rosettadb -s 1ubiA.pdb -score_app:linmin -out:output –out:prefix linmin_

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trying to create heme.params

Following advice on a thread from a year ago, I created a mol2 file from a heme ligand pdb. When I try to create the params file, it told me:
/usr/ros/rosetta_source/src/python/apps/public/molfile_to_params.py hemf.mol2
Traceback (most recent call last):
File "/usr/ros/rosetta_source/src/python/apps/public/molfile_to_params.py", line 1323, in ?
sys.exit(main(sys.argv[1:]))
File "/usr/ros/rosetta_source/src/python/apps/public/molfile_to_params.py", line 1254, in main
molfiles = list(read_tripos_mol2(infile, do_find_rings=False))

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Pyrosetta2

Hi,

I am trying to execute the commands on pyrosetta 2 from tutorial .

After executing the command pose = Pose ("1GFL.pdb") I am getting the following errors :-

---------------------------------------------------------------------------
ArgumentError Traceback (most recent call last)

/examples/ in ()

ArgumentError: Python argument types in
Pose.__init__(Pose, str)
did not match C++ signature:
__init__(_object*, core::pose::Pose src, unsigned int residue_begin, unsigned int residue_end)

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