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Hi all,

I am attempting to predict the conformations of an enzyme after a single mutation. I have been using pymol to place the mutation into the protein and then I use the rosetta relax application to optimize the structure. Is this a valid way of performing this technique? Or should I be using rosetta scripts and repack the sidechains instead. I am worried that the relax protocol may not be able to optimize the residue if pymol puts it in a conformation that is far away from the optimal conformation.

Thank you!

Hello,

I am attempting to follow a recent publication released by the Baker group. I am using this cst file to constrain an iron atom to a histidine:

https://github.com/ikalvet/heme_binder_design/blob/main/theozyme/HMM/HMM_His.cst

I have renamed the HMM residue to match with my ligand name.

Hello, 

I'm attempting to compare protein-protein docking at pH 7 / 11. I've protonated my structures using PROPKA and have performed pre-packing and docking using the following commands:

docking_prepack_protocol.static.linuxgccrelease -database /apps/local/biology/rosetta/2020.11/bundle/rosetta_bin_linux_2020.11.61179_bundle/main/database/ -in:file:s model_5.pdb -unboundrot unbound_rotamers.pdb -nstruct 25 -partners A_B -ex1 -ex2aro

Hello,

I am attempting to use the GALigandDock mover to perform dockings of a metal ligand similar to heme. I am following this paper: https://pubs.acs.org/doi/suppl/10.1021/jacs.3c02742/suppl_file/ja3c02742_si_001.pdf.

I generated a params file using the molfile_to_params script, and proceeded to use the exact same command and docking xml file.