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Rosetta Server

Support for local install of ROSIE?

Category: 
ROSIE

Hello,

Is ROSIE generally available to install and run locally? The original publications provides steps for setting up a test VM to develop protocols, but this does not seem like a production capable system.

I am not a Rosetta user but have been asked to see if we can run ROSIE on a local cluster. 

 

Thanks,

Jim

Post Situation: 

ddG_RNA final energy different when modeling WT sequence

Category: 
ROSIE

Hi, I have been using the ddG_RNA tool within ROSIE to calculate relative affinities for my protein and a list of mutant RNAs. Included in the text file list is the WT sequence that is also specified in the PDB file. Based on how I understand the tool works, the ddG bind score for this RNA should be 0, since the value is relative to the WT sequence. Instead I get a score of 3.36. Any idea on why this would be happening? 

Post Situation: 

getting right protonation state from PKa of Rosie

Category: 
ROSIE

Hello,

Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?

Also, there are two options in pKa program in ROSEI:

1.Pack side chains and protonation states of the residues neighboring the target residue during pKa calculations

2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pKa calculations

 

which one should  we use to get the right protonation state?

 

Post Situation: 

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