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scorefunction Talaris2013

Category: 
Scoring

Hi,

I'd like to use new scorefunction from article by O'Meara et al., 2015, from JCTC. Acording to supplementary info the published ElecHBv2 is the Talaris2013. There is missing line 'yhh_planarity 0.5' in my installation (in comparison with published article). Should I add this line or is it set there by default? what does this line mean.

thanks,
David

Post Situation: 

Reproduce Robetta's ddg values of interface alanine scan using Rosetta?

Category: 
Docking
Scoring

Is there a protocol on Rosetta to obtain Robetta's (http://robetta.bakerlab.org/) ddg's calculations of interface alanine scan functionality?
I don't care if they use an older version of Rosetta. I just want to obtain ddg's values that are as close as possible to those returned by Robetta. What protocol do they use?

Post Situation: 

Different scoring applications (score vs score_aln vs score_jd2, etc.)?

Category: 
Scoring

What's the difference between the different scoring applications?

In my bin folder I find the following scoring applications:

score, score_aln, score_aln2, score_jd2.

What's the difference between them?

(I am omitting the trailing .default.linuxgccrelease, or mpi.linuxgccrelease, since I know those denote parallel vs non-parallel versions)

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: 

Change in binding energy after mutation in interface?

Category: 
Scoring

I have the .pdb structure of a complex of two chains.
I want to try the effect of a mutation in one of the interfaces on the binding energy. I am new to Rosetta. Can someone explain step by step how to compute this delta-delta-G?
Thanks.

Post Situation: 

How to eliminate "NUL"s when scoring PDBs?

Category: 
Scoring

Dear friends,
Can I ask how to eliminate "NUL"s when scoring PDBs? When I want to score PDB files, I have tried

1) -s /mnt/hgfs/test/name.pdb
2) -s /mnt/hgfs/test/*.pdb # for all the PDB files in the "test" folder
3) -l /mnt/hgfs/test/list.txt

Post Situation: 

Memory leak? Memory consumption rises quickly when using JD2 app(s)

Category: 
Scoring

Hey!

I don't know if this is a known issue or not, but when I run score_jd2 with a -in:list:l I get increasing memory consumption, which passes 1.4g (RES column untop `top`) within a minute. Using score with same flags has constant memory usage. I did this check because a JD2 app I'm developing also showed increasingly high memory usage, so I suspect it's a JD2 issue (?)

Post Situation: 

Converting charmm parameter files (.par)

Category: 
Scoring
Non-Canonical Peptides

Is there perhaps a (python) script lying around somewhere in the src distribution to convert charmm parameter files (.prm) into mm_torsion_params.txt and mm_atom_properties.txt (in the database directory database\chemical\mm_atom_type_sets\fa_standard)?
I have added the MM parameters for R1A and now I naturally have a lot of missing types for the mm_* score terms. I’m thinking the easiest way to sort this out is just to regenerate the mm_torsion_params.txt and mm_atom_properties.txt from my working charmm parameter files?

Post Situation: 

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