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unknown constraint function type: AtomPair ?

Hi, when I tried to use constraints files with loopmodel, rosetta give the error message:

ERROR: FuncFactory: unknown constraint function type: AtomPair
ERROR:: Exit from: src/core/scoring/constraints/ line: 65

Could you help me to find out what's the problem?
Thank you very much!

Post Situation: 

optH flag makes hydrogen bond energy scores worse...

I was trying to run rosetta.score with no_optH = false. However, when compared with the energies without hbond optimization, the hydrogen bond energies get worse, while the other components are unchanged. I have attached the input pdb file below.

Here are the command lines:
rosetta.score -database /usr/local/rosetta/3.3/rosetta_database/ -in:file:s test.pdb -out:output -no_optH true # Turn off hbond optimization
rosetta.score -database /usr/local/rosetta/3.3/rosetta_database/ -in:file:s test.pdb -out:output -no_optH false # Turn on hbond optimization

The output score file is:

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Output different favored solutions with PackRotamersMover design


I'm trying to use PackRotamersMover to mutate a serials of mutatable residues into the predefined residues. Here is part of the core codes:

task = TaskFactory.create_packer_task(mutant_pose)
for i in range(1, mutant_pose.total_residue() + 1):
# only perform design for the mutatable residues
if i in mutation_positions:
# only mutate to specific amino acids types, like ["A", "K", "F", "S", "T", "K", "I"]
aa_allow = [False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False]

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Rosetta 3.3 installation in linux


I 'm experiencing an error with Rosetta 3.3 installation in CentOS (free OS of Red hat Enterprise) virtual machine. Its version is 5.8 for a 32bit windows machine. Once i successfully installed scons, i ran this command
"scons bin mode=release" to install rosetta with root permissions in my virtual machine. After a 2 hour compilation, it gave an error saying that it couldn't find "lz" file in my root directory. Below is the error message. Any help on this is appreciated.

/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status

Post Situation: 

Docking structures with ligands in cryo-EM maps

Greetings Rosetta gurus-

We are attempting to use Rosetta 3.3 to flexibly dock crystal structures into relatively high resolution (around 4.8 Angstroms) cryo-EM maps. Our protein of interest binds and hydrolyzes GTP, and oligomerizes in a nucleotide-dependent manner. We have cryo-EM structures of the protein in GDP and GTP states (bound to a non-hydrolyzable analog) in physiological oligomers, and crystal structures of the protein in both nucleotide states in non-physiological conformations/oligomerization states.

Post Situation: 

RosettaSurface in 3.4?


I would like to dock a short (12AA) peptide sequence to a few model inorganic surfaces.

It appears that similar simulations are being done by Jeff Gray's group with RosettaSurface, but its most recent implementation (and tutorial!) seem to be written for Rosetta 2.3...

A closer look at my installed version (3.4) reveals a surface_docking folder in /src/protocols/, but I cannot seem to find any corresponding executables.
Can anyone comment as to the availability and/or implementation of protein-surface docking in Rosetta 3.4?

Post Situation: 

where to look for positive sign for solution in mr-rosetta3.4?

I set up mr-rosetta which is running over 5 days and I guess it should be keep
running for very long time (ran it on a local machine with single processor.
260 residues, 1MOL/Asy). My question is where to look for the positive sign:

So far, the LLG scores from phaser are very low: 2.31-27.1;

From rebuild:

Run_1: ROSETTA SCORE: -1273.01;
Run_2: ROSETTA SCORE: -1427.29;
Run_3: ROSETTA SCORE: -1468.84
Run_4: in running

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Using mode=profile

Thanks in advance.

I need to see which functions are using the most time so I compiled with:

scons mode=profile extras=opencl bin

That was successful and I ran my program:

~/rosetta_source/bin/ragul_darc_run.opencl.macosgccprofile -database ~/rosetta_database/ -input_protein_file 2YXJ.pdb -input_ligand_file ZINC01350605_0001.fa.pdb -extra_res_fa ZINC01350605_0001.fa.params

That was successful and it created a file gmon.out.

But I'm not sure how to work with this. My understanding of gprof is that I need a command like:

gcc -g -pg executable.exe gmon.out

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Error running design in 3.4

I'm just getting started running 3.4. Compiled and tried to run fixbb.linuxgccrelease with a flags file and got this error. Could someone please suggest solutions.

ERROR: Unable to open weights/patch file. None of (./)standard or (./)standard.wts or ~/rosetta3.4/rosetta_database/scoring/weights/standard or ~/rosetta3.4/rosetta_database/scoring/weights/standard.wts exist
ERROR:: Exit from: src/core/scoring/ line: 2835

Post Situation: 


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