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Loop Modeling

why energy is positive?

Category: 
Loop Modeling

Hello:

I am using kic loop protocol to refine a big loop with 12 aa with rosetta. I noticed that the energy is positive from generated .PDB file:

#END_POSE_ENERGIES_TABLE ./my_0002.pdb
chainbreak 0.00388937
loop_cenrms 0
loop_rms 0
total_energy 189.805

Shouldn't it be a negative value in principle?

Post Situation: 

Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

Post Situation: 

About missing disulfide partners for residue...

Category: 
Loop Modeling

Dear experts,

I'm trying to evaluate the energy of a 12 residues loop (residues 48-59) without considerint its environment. This loop contains one disulfide bond between residues 48 and 111. Since this bond links one loop CYS with another CYS located outside, when I trim the loop (dummy) from the full structure (pose) with grafting functions:
rosetta.protocols.grafting.delete_region(dummy,60,pose.total_residue())
rosetta.protocols.grafting.delete_region(dummy,1,47)

and I evaluate energy:
scorefxn(dummy)

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crazy loopmodel: linear output pdbs

Category: 
Loop Modeling

Hi there,
I've just fresh installed the last rosetta version (2014.35) and can't be able to appropriately run protocols that used to work in previous versions. It doesn't matter if I run single or mpi binaries. Loopmodel is running pretty well without warnings, however, the output pdbs are just linear aa sequences. Flags file is in attachment but I could share the entire directory by email. I woulld appreciate if someone who has experienced such problem could share the solution.
Best,

Post Situation: 

Error encountered during Rosetta loop modeling

Category: 
Loop Modeling

Hi everyone,

I'm trying to run Rosetta kinematic loop on my computer but I got an error message after few seconds:

ERROR: Cannot open PDB file "input_pdb"
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 184

The comand that I have used and the screenshot of the error page is shown below:

Post Situation: 

Loop modeling script - unwanted change of amino acid identities

Category: 
Loop Modeling

When running the Loop Modeling script on my protein of interest, the identity of the amino acids in the loop changes when it generates the full atom model from the centroid model. In other words, in the centroid model the amino acids are equivalent to the protein sequence from the original PDB, but they are "mutated" in the FA model (often to lots of G's). Is there a way to prevent this from happening?

Post Situation: 

Efficient local energy computation

Category: 
Loop Modeling

Dear experts,

I need the relative energy of several thousands of conformations of the same 10-residues loop including its static environment. However, I've only found the way to get the absolute energy of the complete structure. This seems a waste of time since most of the inter-residue energy terms are just the same. Is it possible to efficiently compute the energy of a small loop while taking into account its environment in PyRosetta? How?

Thanks a lot!
- Mon

Post Situation: 

Script for loop modeling: how to define loop sequence

Category: 
Loop Modeling

In the tutorial on the loop modeling, loop is defined by the fold tree in the loaded from pdb-file pose that already have residues that are "loop" and are normally missing. If I have a structure, where the loop is missing, how do I define it? As far as I understand, there's no way to do this from sequence, Do I have to make a "fake" loop structure before obtaining a possibility to really model it?

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Possible Shellshock Patch problem results in no output files being written

Category: 
Loop Modeling

Folks,
In September 2014 (before shellshock patch) a user ran a Loop modeling job on our system (rhel 6.3 IBM Platform HPC 4.1.1.1)
The Rosetta version is rosetta_2014.30.57114_bundle
The user is running minirosetta.mpi.

the command is:
mpiexec -launcher ssh -f /PATH/machines -n 50 -ppn 8 /PATH/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.mpi.linuxgccrelease @/PATH/DGCR8_NOE_10172014/2LZM_broker_cst.options -database /PATH/rosetta_2014.30.57114_bundle/main/database

the options file looks like this

Post Situation: 

Problem in using "loopmodel" application to add missing residues

Category: 
Loop Modeling

My problem is with flags -max_helix_melt and -max_strand_melt while creating the loopfile. If I take the default values (-1), it is creating the loopfile with no LOOP information. I have tried with other values which did not give me the correct LOOP information. How should I determine the correct values for these flags to get the correct loopfile. Please suggest.

Post Situation: 

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