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Chemically Modified Residues

Error reading new residue .param file

Category: 
Chemically Modified Residues

Hello,

I am trying to run a point mutant scan on a GFP variant. I created a CRO.param file for the GFP chromophore using InteractiveRosetta. I have attached the CRO.param file as a .txt file. First, I tried putting the CRO.param file in the rosetta database in the l-caa folder in residue_types. I added a line within residue_types.txt as well to include the CRO.param file. I then tried to run the point mutant scan - input here:

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hydroxyproline patching problem

Category: 
Chemically Modified Residues

Hello All

My docking_prepack application is incorrectly patching the hydroxyproline residues. Although the log file indicates that the full-atom patch is correctly read from the fa_standard/patches and also successfully patched, the output prepacked file contains a bond between the CD as well as CG to the OD1 of the HYP residue.

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molfile_to_params script error

Category: 
Chemically Modified Residues

Greetings, I've been following the "design with non-canonical aa" demo (located on demos/public/design_with_ncaa) in order to set parameters for a custom residue "CYM", which is a deprotonated cysteine. Yet I got stuck in the last step namely, when I try to convert my modified .mol file to params using:

"python molfile_to_params_polymer.py cym.mol --clobber --polymer --no-pdb --name CYM -k cym.kin"

it returns:

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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.

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Nonstandard residue parameters fail

Category: 
Chemically Modified Residues

I'm made parameters for a carboxylated lysine residue as well as parameters for a fluorinated phenylalanine. Both sets of parameters work fine in Rosetta. But PyRosetta throws the following errors when I try to use them or when I add the parameters to the database (whether I use them or not).

>>> res_set = generate_nonstandard_residue_set(['KCX.params','PFF.params'])
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 8524 residue types

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Adding noncanonical amino acid (PCA) to Rosetta 3

Category: 
Chemically Modified Residues

Hi everyone, I'm in the process of trying to incorporate a non-canonical amino acid into Rosetta, namely pyroglutamic acid: (or 5-oxo-L-proline)

http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PCA

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Energy minimization of a crystal structure with residues mutated in pymol

Category: 
Chemically Modified Residues

Hi,

I am working on a protein structure which contains a modified amino acid (lysine covalently bound to pyridoxal phosphate). I mutated some amino acids in the crystal structure using Pymol. Now, I want to perform energy minimization of the entire structure. But I get an error due to the modified lysine. What shall I do ??

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BHARAT

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