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Chemically Modified Residues

Altering substrate specificity

Submitted by bp on Thu, 2016-12-22 02:45
Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

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Rosetta 3 - Applications

Histidine protonation

Submitted by DmitriiN on Mon, 2016-09-26 13:15
Category: 
Chemically Modified Residues

Hello, everyone!

I have histidines in my protein and they seem not to have not a usual "HIS" protonation state. I think it is in "HSD" state, but this seems to be noncanonical. I found the HIS_P.params somewhere in the database, but it doesn't seem to work.

What should I do?

Dmitrii

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Rosetta 3 - General

Histidine phosphorylation by a patch

Submitted by felipet on Sat, 2016-07-09 06:51
Category: 
Chemically Modified Residues

Dear all

I am trying to do some minimizations of a phosphorylated protein in a histidine (modification at the NE2) through a patch. To model phospho-histidine at the NE2, I need to delete the HE2 proton and protonate the ND1.

I've modified the his_methylated.txt patch (which I'm attaching) but it seems that whenever I try to delete the NE2 proton the minimization crashes:

caught exception 

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Rosetta 3 - General

modified Serine: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch error

Submitted by Karol on Wed, 2016-05-04 08:47
Category: 
Chemically Modified Residues

 

 Hello.

 I am parametrizing a new residue, the SER, which would be chemically linked to a ligand 4'-PHOSPHOPANTETHEINE (PNS). The connection invovlves SER (here renamed to SEX) CB and O23 of the ligand. 

I had no problem with parametrizing the ligand. However, I am not able to properly parametrize the SER residue.  The error I get is:

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue TYR:CtermProteinFull 85

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Rosetta 3 - General

Error reading new residue .param file

Submitted by mgrom92 on Tue, 2016-03-22 12:54
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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Rosetta 3 - General

hydroxyproline patching problem

Submitted by aaj on Mon, 2016-02-22 07:33
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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Rosetta 3 - General

molfile_to_params script error

Submitted by pablogalazdavison on Tue, 2015-07-07 21:22
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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Rosetta 3 - Applications

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
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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Rosetta 3 - General

Nonstandard residue parameters fail

Submitted by lah435 on Wed, 2014-08-06 17:53
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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PyRosetta - General

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