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Category: 
Compilation

Where is the main website for PyRosetta?
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Post Situation: 

"Segmentation Fault" error occurred when Running a pilot job

Category: 
Design

Hello everyone! I'm trying to run a command in paper_interface_design_pilot_1000_commands.list generated in step 12 “Running a pilot job”
the commands are as follows:

cd /home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/paper_interface_design_pilot_1000/00000

Post Situation: 

Problem with relaxing a PDB around a chemically bound ligand

Category: 
Small Molecules


Hello,

I have downloaded a PDB with a chemically bound ligand (small molecule)

I have followed (in every way that I can see) all the details presented in the tutorial/demo here:
https://www.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README

Post Situation: 

Match Application Error: Assertion `build_sets_[ build_set_id ].restype().has( "1HA" )` failed

Category: 
Enzyme Design

大家好!

我想为新底物设计甲基转移酶。该酶依赖于小分子作为甲基供体 (SAH)。因此,我使用 -extra_res_fa 参数将 SAH 包含为应用的输入。CST 文件包含三个约束:约束 1 涉及底物和 HIS 残基,约束 2 涉及底物和 ARG 残基,约束 3 涉及底物和 SAH。而SAH位于PDB的最后一个块。

Post Situation: 

Error about rifdocking step 15

Category: 
PyRosetta

I am still working on the Cao protocol. And I ran into another problem. When I ran step 15: Motif extraction. I ran the following command:
/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py -in:file:silent /home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/fd_output_splits/xaa.silent -ref_pdb /home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb -out_prefix mot_

Post Situation: 

Error about rifdocking step 12

Category: 
Design

Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. When I ran the commands, the error occurred: 

basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat
WARNING!! DALPHABALL output nan at index 140724834832176
DALPHABALL output indicies not matching! 1!=140724834832176

Post Situation: 

Error about rifdocking

Category: 
Design

Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. When I ran the commands, the error occurred: 

basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat
WARNING!! DALPHABALL output nan at index 140724834832176
DALPHABALL output indicies not matching! 1!=140724834832176

Post Situation: 

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