I am planning on docking a ligand in a cavity with a heme and a constrained oxygen. Whereas I can make params of ligands and non-canonical residues, I cannot for molecular oxygen (OXY). It is not in the database either. Molfile_to_params.py gives the following
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Dear Rosetta users or developers,
I'm trying to model small, cyclic peptides with the simple_cycpep_predict routine. While I explicitely asked for a terminal disulfide cyclization (using the flag -cyclic_peptide:cyclization_type terminal_disulfide), the output models are cyclized with a mainchain bond (the default n_to_c_amide_bond).
I have a pdb file from CHARMM format. When I use
fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out
I got this:
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 1 A TRP TRP:NtermProteinFull:triazolamerC
core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CT1
and it skipped the first residue TRP.
I am new to Rosetta. I am trying to build a model of my protein but my disulphide bond seems to break after centroid stage (I am quessing here). The disulphide thats breaking is in the loop region I am trying to model. I have googled around and found some suggestions but nothing seems to work for me. Here are my flags:
I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:;
~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol docking_stubs.xml
I'm using pyrosetta compiled from rosetta_src_2017.39. I was wondering whether it's possible to use both talaris2014 and ref2015 in the same script. When I try to set up a scoring function using talaris2014 weights, I get this error:
pyrosetta.create_score_function("talaris2014") ERROR: talaris2014(.wts) requested, but -corrections::restore_talaris_behavior not set to true. This leads to a garbage scorefunction. Exiting.