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Atom-wise energy terms from nearest N-neighbors

Category: 
Scoring

Hello PyRosetta users,

Can you please advise me on how I should go about calculating atom-wise energy terms?

Should I simply sum pairwise energies for the nearest N-neighbours or is there a better way of doing this?

 

Thanks!

Post Situation: 

Protocol for adding/mutating non-canonical AA

Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

Post Situation: 

Protocol for adding/mutating non-canonical AA

Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

Post Situation: 

Should I be stripping water molecules from my input structure for Rosetta Design?

Category: 
Design

So I've ran my fixbb rosetta design script and have been happily doing some analysis work, but it just occured to me that I had stripped all the water molecules from my input protein structure and I'm curious whether that biases the rosetta design in a negative way.

What I want to do with my project is to take a fixed-backbone structure of my choosing, optimize the sidechain identities using Rosetta, and then ultimately express it in a cell to see if the optimized sequence folds back into the original backbone conformation.

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Chain name being read as residue

Category: 
Docking

Hi,

I am attempting a ligand docking run in a P450 docking both the heme cofactor and ligand simultaneously. I was able to have a successful run with just the heme group but when I attempt to add in the ligand I get an error. Currently, I've been getting the error "unrecognized mm_atom_type_name W" where W is the chain name for my ligand. I've attached my docking file, initial structure pdb file, and my options file so they can be looked at to help me resolve this issue. Thanks in advance!

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Problem importing residue params file

Category: 
PyRosetta

I have been trying to load 'HYP.params' for the hydroxyproline residue. According to previous answers in the forum there are 2 options: add the params file to the residue_types folder and editing the residue_types.txt or loading the params file via command lines in pyrosetta. Neither of these options work for me and raise the following error:

Post Situation: 

Loop modeling with constraints

Category: 
Loop Modeling
Constraints

Hi,

I am trying to model a loop with a constraints file (the constraints are for the atoms of the loop).

but every time I get this message:

[FILE]: src/core/pose/util.cc
[LINE]: 704
[START_MESSAGE]
Atom 'OVL1 31' not found

[END_MESSAGE]
[END_CRASH_REPORT]

 

I also tried to set the flag "-constraints:named" to true but it didn't help...

I am using the following command:

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