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Pmut_scan with symmetry

Submitted by felipet on Thu, 2015-02-05 08:53
Category: 
Design
Symmetry

Dear developers

I am trying to use pmut_scan for a symmetric dimer. I don't know if this is possible but when I run it with a symmetry definition file the program crashes with the following message:

protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average_ddG average_total_energy
terminate called after throwing an instance of 'std::bad_cast'
what(): std::bad_cast
Pmut_sym.sh: line 29: 678 Aborted (core dumped) pmut_scan_parallel.default.linuxgccrelease

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Rosetta 3 - Applications

Output structures from docking_prepack_protocol: initial__*.pdb vs prepack__*.pdb, which one should I send to docking_protocol?

Submitted by cossio on Thu, 2015-02-05 07:10
Category: 
Docking

docking_prepack_protocol generates several output pdb structures:

away__*_0001.pdb
away_packed__*_0001.pdb
initial__*_0001.pdb
prepack__*_0001.pdb
*_0001.pdb

where * stands for the name of the crystal structure that was given as input to docking_prepack_protocol.

What are the differences between these .pdb files that docking_prepack_protocol outputs?

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Rosetta 3 - Applications

Calculate_protein_protein_ddg

Submitted by kamau on Fri, 2015-01-30 11:27
Category: 
Design

Dear Rosetta Users
I am trying to utilize the calculate_protein_protein_ddg protocol using the mutation_script.xml protocol on rosetta_2014wk52 build.
However, I am having a problem with mutating chemically modified residue (sulfated tyrosine) into a desired amino acid. I can mutate any non modified canonical amino acid to whichever amino acid I want but not the chemically modified one.

sample tail of output pdb
REMARK DesignRes. # modified amino acid mutation attempt
REMARK DesignRes, 108 H # non modified amino acid mutation attempt

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Rosetta 3 - Applications

Relax with a ligand is messing up the coordinates of the ligand

Submitted by brspurri on Sat, 2015-01-24 12:39
Category: 
Design

Hi there,

 

I am trying to relax my structure which contains a bound ligand.

 

First, I created a LG.params file using:

python /path/to/molfile_to_params.py /path/to/1XKK_ligand.mol2

 

This file (1xKK_ligand.mol2) only contains the coordinates for the ligand from the PDB 1XKK.  molfile_to_params.py outputs the LG.params file as well as a PDB, which looks correct when visualy inspected. This is all expected.

 

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Rosetta 3 - Applications

minirosetta: how to reserve (inter-chain) disulfides after relax ?

Submitted by lanselibai on Sat, 2015-01-24 10:56
Category: 
Structure prediction

(I would appreciate it very much if any of my questions can be answered.)

Dear friends,
I have been trying to reserve the disulfides of my target protein during the minirosetta comparative modelling. However, though I have gone through many posts, I still could not work it out after using several disulfide related flags.

My situation is:

in the target protein:
Light chain (LC): residue 1-214
Heavy chain (HC): residue 215-442

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Rosetta 3 - Applications

force field, energy function

Submitted by masterofpuppets on Wed, 2015-01-21 11:06
Category: 
Structure prediction

Hello everybody,

I am interest in, which force field Rosetta use and which energy functions are applied for a normal abinitio calculation. If I used an abinitio calculation with a metallatom, are there used a other force field for the zinc atom?!
Can anybody advice my a good paper which an easy explanation or something like that?!

many regards

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Rosetta 3 - General

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

Submitted by cossio on Mon, 2015-01-19 07:14
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?

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Rosetta 3 - Applications

FloppyTail as a rosettascripts file

Submitted by tiagogomes89 on Mon, 2015-01-19 02:45
Category: 
Structure prediction

Hello rosetta community,

I was wondering if anyone has a RosettaScripts xml file that emulates de FloppyTail application. I´m currently generating decoys of a two domain protein
with a big disordered linker with the objective of modeling it to saxs data.
I just wanted to gain more control over the process and to see exactly what the application is doing.

Thank you,
Tiago

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Rosetta 3 - Applications

How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?

Submitted by lanselibai on Sat, 2015-01-17 11:19
Category: 
Structure prediction

Dear friends,
I have a Fab (antibody fragment of antigen binding) with two chains(LC 1-214, HC 215-442). An interchain disulfide bond is supposed to form between LC-214-cysteine and HC-434-cysteine. I am using 4KMT as its homology template. In the 4KMT structure, the interchain disulfide bond does exist. However, after replacing the residues with my own residues, the interchain disulfide bond has lost and become "-SH" instead of "-S-S-".

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Rosetta 3 - Applications

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