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Chemically Modified Residues

molfile to params polymer python errors

Category: 
Chemically Modified Residues

I am trying to generate parameters for a non-cannonical amino acid using the molfile_to_params_polymer.py script using python 2.7.5.python molfile_to_params_polymer.py --clobber --polymer --no-pdb --name OCT -k OCT.kin OCT.mol

Edit: this is where I found the python script that is giving the errors.  /path/rosetta_demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py

I get the error:

Traceback (most recent call last):

  File "test_molfile_to_params_polymer.py", line 1995, in <module>

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Using residue patches in AbinitioRelax

Category: 
Structure prediction
Chemically Modified Residues

I am hoping to 'fold' short phosphorylated peptide sequences, and started by generating fragments with SS predictions on the unphosphorylated peptides. For example, I ran this sequence through a local installation of PSIPRED and picked 200 3- and 9-mers:

>1
MKGDAHRYLAEFATG

I checked that the TYR_p:phosphorylated patch was active in the full-atom patches.txt, then created a centroid patch and added it to the patches.txt by analogy to existing patches:

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Do Rosetta support hydroxide(OH-) and oxide(O2-) params?

Category: 
Enzyme Design
Small Molecules
Chemically Modified Residues

Hello All,

For one of my project I need to hydroxide (OH-) and oxide (O2-). EnzDes is failing to take it. 

Error: caught exceptionFile: src/numeric/xyzVector.hh:665Cannot normalize xyzVector of length() zero

Oxide Params
 

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Altering substrate specificity

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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Histidine protonation

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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Histidine phosphorylation by a patch

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

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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