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Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline.
We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.
I am trying to read a pdb file that has a chloride anion important for its structure. The error is that it is not recognized by rosetta, as sometimes happily happen with other small ions. Looking through the database file I found a params file for a chloride ion model, located at: $ROSETTA_HOME/main/database/chemical/residue_type_sets/fa_standard/residue_types/anions/CL.params. The file reads:
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
These are many .wts file in database\scoring\weights.
I don't clearly know which weight is used in which occasions,
and just use score function according to papers.
I read the webpage(https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring)
and its recommend references.
I'm looking at the methods of the following paper:
Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909.
Computational design of environmental sensors for the potent opioid fentanyl.
Bick MJ#1, Greisen PJ#1, Morey KJ2, Antunes MS2, La D1, Sankaran B3, Reymond L4,5, Johnsson K4,5, Medford JI2, Baker D1,6.
and trying to follow along (to eventually adapt it for my own work).
I've hit a snag at one of the commands:
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
I have been trying to use the pepspec application /main/source/bin/pepspec.linuxgccrelease @xyz.options with following as the contents of .options file