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I am trying to generate a ncAA. My current workflow is using a program called iQmol which has a connection to a QChem server, to produce an appropriate mol file. I then use mol_file_to_params.py to get the params files. It creates a params file with all the atoms quite close together. Running mol_file_to_params gives me this output with the attached files:
edanhabel@Edans-MacBook-Pro-2 molfile2params % python molfile_to_params.py iqmol_pymol_aromatic.mol2 -n f5p --clobber --amino-acid PHE
I am trying to parameterize an NCAA which is a result of cyclization of the backbone, rather than just a PTM of an R group. I am using the molfile_to_params_polymer.py script (BTW is there a python 3 version of this script?)
The connection points are at the R group of one residue, though there is a break in the chain (C=O -> C-OH) then a connection point to the nitrogen backbone atom of the subsequent residue.
When I use fixbb to modify to this residue I am getting the error:
I usually use my NCAAs by mutation in the sequences.
Now, I am looking for a way or application in Rosetta to add, not mutation, NCAAs to the N- terminal and C- terminal of the sequences.
The RCSB pdb starts with leu at N- terminal in attached picture that we need to add pyroglutamate before that
I wonder if anyone could let me know how I can add pyroglutamate using params file and rotlib file to the sequence.
I want to model the tetrahedral transition state of an enzyme where serine OG attacks the peptide backbone C atom. In this case the bond order of the backbone C=O bond changes to C-O(H) and the C-O(H) is not in plane anymore.
So far I wrote this patch file and added a hydrogen to the O atom in the input model which is named H01. The patch file is used since I get an error when I don't include it.
I've been trying to insert a beta-amino acid into peptide, let's say, beta-homo-leucine. It seems that a params file for beta-hLeu is needed. Unforutnately, there is no params file for beta-hLeu in database in Rosetta, and molfile_to_params.py only works for alpha-amino acid. I've also visited https://rosie.rosettacommons.org/documentation/beta_peptide_design, but did't find helpful solution. So my question is:
I'm using cyclosporin to as a test case for understanding the design of macrocycles using Rosetta. In the $ROSETTA3_DB/chemical/residue_type_sets/fa_standard/residue_types/cyclosporin directory there are parameters for two cyclosporin specific residues. But when I try to use these residues in my input sequence (ALA LEU LEU VAL BMT LMA GLY LEU VAL LEU ALA), I'm getting this error when I run simple_cycpep_predict:
ERROR: Error! Could not open rotamer library file ncaa_rotamer_libraries/cyclosporin/BMT_Nmethylated.rotlib for read.
Hi, I'm trying to use simple_cycpep_predict to model the conformation of a disulfide linked cyclic peptide. The peptide has an amidated C terminus. I've been trying to get the patch Cterm_amidation working however it appears to ignore the patch.
A sample input sequence is:
CYS ALA ALA ALA ALA CYS ALA ALA ALA:Cterm_amidation
And here's my test input script:
I am running molfile_to_params_polymer.py to get the .params file for my non-canonical aa. But I got the error below. I think it might be due to the long chain of my non-canonical amino acid. I tried to increase the greek letters list in line 1655 of the script, but it did not work. Maybe it needs to modiy several lines of code.
Also, I got large numbers (as you see the error below).Can someone help to modify the code for my non-canonical amino acid to resolve the error?