I am working with a polymer with a non-aminoacidic backbone comprising two subunits, each defined as individual residues. I have already defined the params file for both subunits; however, I am experiencing issues exploring torsions between these connected residues. I am setting the angle movement using pose.conformation().set_torsion_angle(). This function has worked for angles between atoms inside the same subunit. However, when trying to set_torsion_angle() for atoms residing in different residues, I get the following error:
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Hi, I wonder if there is a general way to generate the correct params file of new beta and gamma NCAA ? I am trying to parameterize a customized gamma amino acid residue for GenKIC application. I used the molfile_to_params_polymer.py to generate .params file from the .mol file attached below:
29 28 0 0 1 0 0 0 0 0999 V2000
-5.3100 -4.8280 2.6840 N 0 0 0 0 0 0 0 0 0 0 0 0
I am using an xml script to design macrocycle peptides similar to https://www.pnas.org/doi/abs/10.1073/pnas.2012800118.
The script runs well in my HPC machine until it crashes unexpectedly. Attached is the output with the backtrace of the error. I am using Rosetta version rosetta.source.release-314 r314 2022.11+release.512e589 512e58946eaed9de20d65cdeea465e7690dc9e9a.
I am using the same script with a different peptide sequence and it runs well, until now.
I want to modell the HbA1c (Hb with Galactose bound to the N-Terminal Val) N-Terminal residues.
I can't find a matching paramterset for the Galactose in the database. The to6-*-*-Galp.param is very close except that instead of the O6 atom, the C6 is bound to the N of the Val.
What is the best way to add the right parameters as a new residue type? Copy the to6-*-*-Galp.param files and modify just the atoms bound to the N or start from scratch?
How would the new *.param file look like?
I want to use GenKIC to generate macrocycles of a peptide bound to a receptor with the anchor design approach. Previously, I used simple_cycpep_predict, from the command line, to generate the candidates, but not bound to the receptor.
I want to generate a macrocycle of a 10 residues peptide, that has an amidated C-terminal residue.
For this, I am playing with simple_cycpep_predict with the -cyclic_peptide:cyclization_type sidechain_isopeptide flag to get crosslinked sidechains between positions 5 and 10, i.e, LYS5 ... ASP10 (ASP10 is amidated). I have a lineal peptide pdb of the same sequence that I would use as native). My command line and flags are:
We're trying to incorporate a nonanonical amino acid (3, 5-Difluorotyrosine) in my enzyme design protocol. We've been using the molfile_to_params_polymer.py script provided in the demos folder; however, the params file isn't generating correctly (the file is attached below as DFT.params). When running enzyme design protocol, we get the following error:
"Only the third ICOOR atom in a topology file should list itself as its own dihedral atom"
I've been trying to incorporate a noncanonical selenium-containing residue into my protein sequence, however, when running molefile_to_params_polymer.py I keep getting an error saying "unknown element SE." I've tried looking at the code where the error occurs, and it seems there are a series of elif statements that specify some atoms that are allowed. That being said, I swapped selenium out for xenon (not listed in the code) in the sdf file and the function ran to completion. I've attached a screenshot of my SDF.
I am using the shape complementarity filter to evaluate noncanonical amino acids. For several noncanonicals that contain Chlorine and Fluorine atoms the sc value is -1. I suspect this is due to the code for sc not being compatible with atom types that are not C,N,O,S,and P. Does anyone have a solution or suggestion on how to get sc updated to work with all NCAA's?