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Generating Params File for water molecule

Submitted by Ahmed Raslan on Thu, 2023-08-17 13:13
Category: 
Docking

Greetings,

I'm new to Rosetta, and I'm currently attempting to create a params file for docking water as a secondary ligand in my docking experiment. I'm using the following Rosetta script for this purpose:

Rosetta/main/source/scripts/python/public/molfile_to_params.py -n X00 -pX00 --conformers-in-one-file 0001H2O.mol2 --keep-names --chain D

However, I'm encountering an error message that reads: "ValueError: No acceptable neighbor atoms in molecule!"

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Rosetta 3 - General

Error when using published constraints file

Submitted by Delfosse57 on Thu, 2023-08-17 11:22
Category: 
Design

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.

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Rosetta 3 - General

ValueError("Path %s does not exist!" % path_name) for rna_helix.py

Submitted by kameisel on Wed, 2023-08-16 00:39
Category: 
Structure prediction
Nucleic Acids

Hi everyone,

I want to model helices with rna_helix.py but I get an error that rna_helix.linuxgccrelease isn't in the path where python script is looking for it:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/rna_helix.py", line 27, in <module>

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Rosetta 3 - Applications

RosettaDock - protonation states

Submitted by LWilliamson on Tue, 2023-08-15 08:15
Category: 
Docking

 

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

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Rosetta 3 - General

[ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection!

Submitted by Jane_002 on Tue, 2023-08-08 21:07
Category: 
Docking

Hello

I'm new to Rosetta. I followed the tutorial of RosettaAntibodyDesign and ran the program well, but there was always some ' warnings ' in the log files.

 I extracted some warnings from the log file as below:

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Rosetta 3 - General

GALigandDock errors

Submitted by Delfosse57 on Mon, 2023-08-07 13:16
Category: 
Docking

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.

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Rosetta 3 - General

Rosetta Design: Non-canonical amino acid substrate not accepted

Submitted by Friedrich Ehinger on Fri, 2023-08-04 00:09
Category: 
Enzyme Design

I experience difficulties when submitting an enzyme PDB file with the
substrates AMP and a non-proteinogenic amino acid to the RosettaDesign webserver.
AMP is well accepted but problems arise with the amino acid substrate.

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Rosetta 3 - Applications

Minimizing a Symmetric Structure

Submitted by ammar.x.gilani on Wed, 2023-08-02 11:10
Category: 
Symmetry

Hi, I have a structure with two chains (1 and 2 ) which are identical. My goal is to minimize its structure using FastRelax with a symmetry constraint.

Creating symmetry file: 

make_symmdef_file.pl -p Data/2mcg.pdb -a 1 -i 2 > Data/2mcg.symm

Structure minimization:

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PyRosetta - General

Academic e-mail adress verification

Submitted by Pat21778 on Wed, 2023-08-02 04:11
Category: 
ROSIE

Hi,

Could you please verify my academic email address so that I can access ROSIE via Github?

My institution name: National Center for Tumor Diseases Heidelberg, Germany - an institution of the German Cancer Research Center Heidelberg

Institution domain: @nct-heidelberg.de or @dkfz-heidelberg.de

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ROSIE - General

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