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interpreting score values in silent output file after running abinitiorelax

Submitted by burkheadlab on Wed, 2011-03-09 15:42

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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Rosetta 3 - General

Where is the flag -preserve_input_cb?

Submitted by mdyini on Wed, 2011-03-09 14:40

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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Rosetta 3 - General

Using 2 non-standard residues in one run

Submitted by einew on Tue, 2011-03-08 21:24

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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Rosetta 3 - General

Docking 2 proteins including ligands

Submitted by einew on Tue, 2011-03-08 13:33

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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Rosetta 3 - General

cluster error

Submitted by albumns on Sun, 2011-03-06 03:02

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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Rosetta 3 - General

Trouble building rosetta in windows with cygwin

Submitted by burkheadlab on Fri, 2011-03-04 11:27

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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Rosetta 3 - Build/Install

-score_app:linmin flag not working

Submitted by fglaser on Tue, 2011-03-01 06:04

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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Rosetta 3 - Applications

trying to create heme.params

Submitted by einew on Mon, 2011-02-28 13:33

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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Rosetta 3 - General

Pyrosetta2

Submitted by bharat_46010 on Mon, 2011-02-28 05:00

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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