cartesian_ddg output – Rosetta Commons

This topic has 2 replies, 2 voices, and was last updated 6 years, 3 months ago by Anonymous.

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- October 11, 2018 at 9:58 pm #3020
  Anonymous
  I am following the protocol
  
  https://www.rosettacommons.org/docs/latest/cartesian-ddG
  
  to predict the ddG of a monomer after a point mutation. I am using Rosetta 3.10.
  
  The output file, mutfile.ddg, looks like this:
  
  COMPLEX: Round1: WT …
  
  COMPLEX: Round2: WT …
  
  COMPLEX: Round1: MUT_1ALA …
  
  etc.
  
  Instead of COMPLEX, I was expecting to see lines beginning with
  
  BEFORE_JUMP: RoundX:
  
  as in the documentation for a monomer. Is there something I am doing wrong that the program is computing an interface ddg instead of a monomer stability ddg?
  
  Here is the command I am running
```
cartesian_ddg.static.linuxgccrelease 

 -database $ROSETTADB 

 -s structure.pdb 

 -ddg:mut_file $MUTFILE  

 -ddg:iterations 3 

 -ddg::cartesian 

 -ddg::dump_pdbs true 

 -bbnbr 1 

 -fa_max_dis 9.0 

 -beta_cart
```
  and the mutfile
  
  total 1
  
  1
  
  S 1 A
- October 11, 2018 at 10:15 pm #14461
  Anonymous
  How recent is your version of Rosetta. There were some updates to the ddg code that were accidentally put on by default that could be causing this behavior. Can you try adding the flag -ddg:legacy true and see if that produces the expected output?
  - October 12, 2018 at 11:43 am #14463
    Anonymous
    It’s Rosetta 3.10.
    
    -ddg:legacy true gives an error:
    
    File: src/utility/options/OptionCollection.cc:1324
    
    Option matching -ddg:legacy not found in command line top-level context
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