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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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PyRosetta - General

example scripts for comparative modeling

Submitted by fglaser on Sun, 2011-02-27 21:50

Hi All,

I am completely new to Rosetta, so forgive me for the trivial questions. I would like to run comparative modeling with rosetta, does anybody has a good simple tutorial or script examples?

I am aware about the online manual info, but it is not detailed enough...

Every information will be highly appreciated!

Have a good day,

Fabian Glaser
Technion, Israel

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Rosetta 3 - Applications

ERROR READING PDB FILE

Submitted by asmi on Sat, 2011-02-26 07:23

I am new to rosetta3.0. As i am trying to perform denovo modelling of RNA molecule my script is giving an error again and again like this:

ERROR: unrecognized aa r
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 476

I have already changed the PDB file format so that res name reads rA, rG, rU, and rC. But still i am getting this message.Can someone suggest whats going wrong?

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