I don't have a problem*, I just wanted to link to a possibly useful resource. Namely, I was playing around with primeval genetic codes and I wanted to to know what the 3-letter code was for one amino acid. As a result I wrote a small script to make a table of images, filenames and three letter codes.
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Chemically Modified Residues
I have a protein which has a few PTMs in the form of sugars, and I have therefore started experimenting with sugars in PyRosetta. I have found a very nice guide:
which I have used as a starting point together with the documentation e.g.
I am following the protocol for Relax Around A Chemically Bound Ligand
/path/rosetta/3.9/main/source/bin/relax.static.linuxgccrelease -s AcpP-TesA-C8.pdb -in:file:fullatom -extra_res_fa ./LG.params -cst_fa_file chemical_bond.cst -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false -overwrite
and I get the error
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>
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:
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:
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
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.