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Rosetta 3 - Applications

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:18
0
17,017 by admin
Fri, 2015-09-04 16:17
Normal topic analyze_flex_ddG.py
by valebut » Tue, 2023-11-28 04:30
1
57 by Aleksandra Panfilova
Tue, 2023-11-28 05:34
Normal topic Is Biopython required to run pdb_renumber.py?
by ljjjxay » Wed, 2023-11-22 20:00
5
107 by rmoretti
Mon, 2023-11-27 07:26
Normal topic I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi
by Edward » Sat, 2023-11-25 04:58
1
47 by Edward
Sat, 2023-11-25 05:17
Normal topic Error with SapScoreMetric (SimpleMetric sap_score not found in basic::datacache::DataMap)
by Seongsung » Fri, 2023-11-24 05:09
0
33 by Seongsung
Fri, 2023-11-24 13:14
Normal topic Cannot install DAlphaBall
by gerdos » Fri, 2023-10-13 07:55
1
339 by Seongsung
Fri, 2023-11-24 04:52
Normal topic nomenclature question in molfile_to_params_polymer.py in ncaa design
by lei » Tue, 2023-11-21 09:47
2
81 by lei
Wed, 2023-11-22 06:23
Normal topic Match: Outputs with 0 hits for cst and clashes with sidechains
by uka147 » Wed, 2023-11-08 06:11
0
96 by uka147
Thu, 2023-11-09 01:36
Normal topic 'Use_filters true' option - failure of AbInitio Relax application
by Corvin » Wed, 2023-11-08 06:34
0
61 by Corvin
Wed, 2023-11-08 06:34
Normal topic Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"
by vitoralmeida1808 » Mon, 2023-11-06 09:43
0
64 by vitoralmeida1808
Mon, 2023-11-06 09:43
Normal topic Are catalytic residues mutatable?
by uka147 » Thu, 2023-10-26 03:49
3
296 by uka147
Mon, 2023-10-30 01:53
Normal topic Docking to TM protein plus lipid bilayer
by renedominik » Tue, 2019-03-12 06:58
4
3,205 by elpipasp
Thu, 2023-10-19 04:37
Normal topic ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 42
by yliang20 » Wed, 2022-06-15 22:22
2
1,070 by jxw
Wed, 2023-10-11 10:04
Normal topic Dock cyclic peptide with non-canonical amino acids to protein target using rosetta flexpepdock?
by lei » Mon, 2023-09-11 23:34
2
275 by lei
Wed, 2023-09-13 19:35
Normal topic ValueError("Path %s does not exist!" % path_name) for rna_helix.py
by kameisel » Wed, 2023-08-16 00:39
2
296 by kameisel
Wed, 2023-09-13 02:16
Normal topic FixedBB design output no beta strands
by tkoh » Fri, 2023-08-25 01:02
1
241 by rmoretti
Tue, 2023-08-29 20:13
Normal topic How do I compare the results of InterfaceAnalyzer using different trimers as input?
by franz72 » Sun, 2023-08-06 10:10
0
184 by franz72
Sun, 2023-08-06 10:10
Normal topic Rosetta Design: Non-canonical amino acid substrate not accepted
by Friedrich Ehinger » Fri, 2023-08-04 00:09
2
326 by Friedrich Ehinger
Fri, 2023-08-04 08:38
Normal topic Multistate design issues with -run:msd_job_dist option and MSDMover
by elaine.thai » Wed, 2020-05-13 18:07
2
2,849 by Jane_002
Thu, 2023-08-03 19:47
Normal topic RECCESS-Rosetta Segmentation Fault with nonnatural residues
by skorro » Tue, 2023-07-25 17:13
1
270 by skorro
Fri, 2023-07-28 12:20
Normal topic Antibody Structure Prediction - Error on antibody_H3 step: "Option matching -antibody:remodel not found in command line"
by ramon-arg » Mon, 2023-07-24 17:56
0
170 by ramon-arg
Mon, 2023-07-24 17:56
Normal topic ERROR: ResidueType::add_ring: Requested atoms don't exist in this ResidueType!
by walidabualafia » Thu, 2023-07-20 09:44
1
227 by rmoretti
Thu, 2023-07-20 10:08
Normal topic fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
by yueyuedake » Wed, 2023-07-12 03:36
6
536 by yueyuedake
Sun, 2023-07-16 19:17
Normal topic rosetta_cm - ERROR: Assertion `tlen < slen` failed on File: src/core/fragment/util.cc:177
by ramon-arg » Thu, 2023-07-13 18:41
2
308 by ramon-arg
Fri, 2023-07-14 07:47
Normal topic Memory Leak in FragmentPicker.cxx11thread application
by Corvin » Tue, 2023-07-11 06:04
0
190 by Corvin
Thu, 2023-07-13 05:30
Normal topic PyIgClassify cannot renumber and label CDRs my Nanobody-Antigen complex for RabD
by WBNeT » Fri, 2023-07-07 10:58
1
281 by jadolfbr
Mon, 2023-07-10 09:05
Normal topic EMERALD method not working, Rosetta version not available for download
by seba » Thu, 2023-05-04 08:14
6
935 by rmoretti
Mon, 2023-07-10 08:57
Normal topic cluster docked pdbs
by kwu030 » Wed, 2023-06-14 22:48
1
382 by rmoretti
Wed, 2023-06-28 12:36
Normal topic Generating a new Vall database
by vijay.anand » Tue, 2023-06-20 12:08
0
227 by vijay.anand
Tue, 2023-06-20 12:08
Normal topic Silent File Scores Missing: RNA Protein Complex Predition
by axio23 » Fri, 2023-06-16 05:45
0
237 by axio23
Fri, 2023-06-16 05:45
Normal topic non-zero ddG of binding even without mutations
by top-gun98 » Wed, 2023-06-07 17:19
0
247 by top-gun98
Wed, 2023-06-07 17:19
Normal topic CC (or similar) calculation for cryoEM fitting
by almeida85 » Tue, 2023-05-16 01:32
2
445 by almeida85
Tue, 2023-05-23 08:23
Normal topic dG_separated values comparison
by almeida85 » Mon, 2023-04-24 03:34
0
359 by almeida85
Tue, 2023-05-16 01:02
Normal topic Error with xml script
by almeida85 » Tue, 2023-03-28 01:53
0
406 by almeida85
Tue, 2023-05-16 01:00
Normal topic Simple_cycpep_predict with crosslinker BBMB
by Ken » Tue, 2023-05-09 08:52
0
301 by Ken
Tue, 2023-05-09 08:52
Normal topic Docking one protein into interface between two other proteins
by Cheems » Sat, 2023-05-06 09:49
3
555 by rmoretti
Mon, 2023-05-08 13:14
Normal topic Missing atoms, unable to fill in missing atoms
by kwu030 » Fri, 2023-05-05 13:41
1
328 by rmoretti
Fri, 2023-05-05 13:44
Normal topic unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file
by Sajjad » Wed, 2022-11-30 11:40
1
3,907 by FJOM
Wed, 2023-05-03 07:21
Normal topic Problems with ligand when running RosettaLigand
by Cat » Mon, 2013-05-20 15:58
6
6,501 by Aben
Tue, 2023-04-18 01:31
Normal topic XML validation failing
by mb0261 » Fri, 2023-04-14 14:53
11
1,372 by mb0261
Mon, 2023-04-17 17:38
Normal topic error in loop remodeling
by syntekabio2019 » Wed, 2023-04-05 01:00
0
281 by syntekabio2019
Wed, 2023-04-05 01:01
Normal topic Protein Protein Docking with Linker
by mrinal » Mon, 2023-03-20 15:58
0
623 by mrinal
Mon, 2023-03-20 15:58
Normal topic core.pose.util: (0) {0} [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard
by ldx022 » Thu, 2023-03-16 04:13
0
1,002 by ldx022
Thu, 2023-03-16 04:13
Normal topic Lots of Prepacking Jobs for Snugdock Failing
by katherinemccoy » Tue, 2023-02-28 18:17
0
2,184 by katherinemccoy
Mon, 2023-03-13 19:10
Normal topic ReplicaDock 2.0 Native vs Input Structure Flags Confusion
by katherinemccoy » Tue, 2022-12-27 06:42
2
4,385 by katherinemccoy
Tue, 2023-02-28 18:19
Normal topic how to control alignment for energy_based_clustering
by xfradera » Tue, 2023-02-28 10:13
0
1,738 by xfradera
Tue, 2023-02-28 10:13
Normal topic ligand_docking
by yang » Thu, 2023-02-16 04:37
2
2,148 by yang
Wed, 2023-02-22 19:18
Normal topic St13runtime_error in Rosetta ligand docking
by syntekabio2019 » Thu, 2023-02-09 18:18
2
2,754 by syntekabio2019
Sun, 2023-02-19 18:39
Normal topic How to change the axes of "-spin" in docking_protocol
by Zehui Zhou » Mon, 2023-02-13 22:06
0
1,901 by Zehui Zhou
Mon, 2023-02-13 22:06
Normal topic Comparing a prediction to the native structure and calculate RMSD for RNA
by danwolf_33 » Thu, 2023-02-09 09:32
0
1,760 by danwolf_33
Thu, 2023-02-09 09:34
Normal topic relax protein with multi-conformer bound ligand
by xfradera » Thu, 2023-01-12 09:10
4
3,040 by rmoretti
Mon, 2023-02-06 15:06
Normal topic prepack - residue count fails
by xfradera » Fri, 2023-01-27 06:36
0
997 by xfradera
Fri, 2023-01-27 06:36
Normal topic Different scoring applications (score vs score_aln vs score_jd2, etc.)?
by cossio » Fri, 2014-12-26 07:19
3
4,449 by Patrícia Antunes
Fri, 2023-01-20 11:55
Normal topic snugdock(sequence position requested was greater than the number of residues in the pose)
by lei » Thu, 2023-01-12 01:40
5
2,125 by lei
Fri, 2023-01-20 08:11
Normal topic Grafting using antibody.mpi.linuxgccrelease and specifying custom template which doesnt have pdb id.
by SubhaK » Wed, 2023-01-18 23:33
0
826 by SubhaK
Wed, 2023-01-18 23:33
Normal topic Snugdock Error: The sequence position requested was greater than the number of residues
by stannowitz » Tue, 2023-01-17 07:37
0
956 by stannowitz
Tue, 2023-01-17 23:48
Normal topic RosettaCM Ignoring Ligand
by Delfosse57 » Sun, 2022-12-04 12:05
0
3,823 by Delfosse57
Sun, 2022-12-04 12:05
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09
3
4,620 by Sajjad
Wed, 2022-11-30 11:50
Normal topic The confussion about an example in tutorial in Rosetta Virtual Workshop 2020
by ldx022 » Tue, 2022-11-29 04:58
3
4,077 by ldx022
Tue, 2022-11-29 08:38
Normal topic Score.sc file showing total score 0 for all protein structures created
by aanshi » Wed, 2022-11-23 11:13
1
3,263 by nannemdp
Mon, 2022-11-28 09:39
Normal topic Help to understand docking results
by rtorquato » Fri, 2022-11-25 12:05
0
1,337 by rtorquato
Fri, 2022-11-25 12:05
Normal topic snugdock: constrained backbone
by mahendra » Mon, 2022-11-14 02:51
0
1,631 by mahendra
Mon, 2022-11-14 02:51
Normal topic Ligand Rotamer Control in Macther
by Hirbond » Tue, 2022-10-25 13:01
0
1,630 by Hirbond
Wed, 2022-10-26 12:57
Normal topic Setting pivots points for GenKIC
by almeida85 » Tue, 2022-10-25 02:32
0
1,554 by almeida85
Tue, 2022-10-25 02:32
Normal topic Small molecule dimer/trimer/etc docking
by lukasz » Tue, 2022-10-04 06:49
1
1,540 by rmoretti
Tue, 2022-10-04 07:57
Normal topic Symmetry definition question
by mrconde96 » Sun, 2022-10-02 05:34
0
1,245 by mrconde96
Sun, 2022-10-02 05:34
Normal topic Old Knotfind algorithm
by Martin Floor » Thu, 2022-09-22 07:28
1
946 by rmoretti
Fri, 2022-09-23 09:38
Normal topic ReplicaDock2.0 demo fails with MPIFileBufJobDistributor: (1) [ ERROR ]
by erpannec » Tue, 2022-08-09 05:42
4
1,451 by erpannec
Thu, 2022-09-15 05:17
Normal topic Prepacking a macrocycle for docking / preserving cyclization
by almeida85 » Thu, 2022-09-08 06:54
0
691 by almeida85
Thu, 2022-09-08 06:54
Normal topic Trehalose
by jpfuenzalidawx » Thu, 2022-09-08 00:49
0
650 by jpfuenzalidawx
Thu, 2022-09-08 00:49
Normal topic Macrocycle from a C-terminal amidated peptide
by almeida85 » Thu, 2022-08-18 07:53
0
775 by almeida85
Thu, 2022-08-18 07:53
Normal topic Docking HeparinSulfate to proteins using GlycanDock
by GebauerJ » Tue, 2022-08-16 07:44
0
747 by GebauerJ
Tue, 2022-08-16 07:44
Normal topic RIFdocking:Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/
by sia » Tue, 2022-08-02 20:06
2
1,464 by SeongRyeong Go
Mon, 2022-08-15 18:31
Normal topic simple_cycpep_predict - Design mode - The base name "ARG" was added more than once
by almeida85 » Thu, 2022-08-04 02:57
4
1,367 by almeida85
Thu, 2022-08-11 00:58
Normal topic Urgent issue: Error with submitting a new Rosetta-Vienna RNP-ddG job
by eyaaaan » Sun, 2022-08-07 22:03
0
741 by eyaaaan
Tue, 2022-08-09 21:59
Normal topic Nanobody design
by chandana » Tue, 2022-08-09 20:36
0
993 by chandana
Tue, 2022-08-09 20:36
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
6
3,728 by chandana
Tue, 2022-08-09 20:27
Normal topic Unknown Element "SE" when generating NCAA params file containing selenium
by liuwenxi » Thu, 2022-08-04 16:24
2
1,023 by liuwenxi
Fri, 2022-08-05 09:50
Normal topic Include MHC alpha helices in loop modelling protocol for pMHC complex
by Roberto » Thu, 2022-08-04 07:22
0
707 by Roberto
Thu, 2022-08-04 07:22
Normal topic pMHC modelling
by Roberto » Thu, 2022-08-04 07:11
0
627 by Roberto
Thu, 2022-08-04 07:11
Normal topic CS-Rosetta cofactor
by martongadanecz » Wed, 2022-08-03 01:05
0
679 by martongadanecz
Wed, 2022-08-03 01:05
Normal topic errors about RIFdocking
by sia » Sun, 2022-07-24 20:45
6
1,998 by sia
Tue, 2022-08-02 20:08
Normal topic Benchmarking Rosetta DDG Methods
by sareeves96 » Fri, 2022-07-29 09:55
0
774 by sareeves96
Fri, 2022-07-29 09:55
Normal topic Expected density
by GabrielDucrocq » Thu, 2022-07-14 06:38
1
842 by matteoferla
Wed, 2022-07-20 10:50
Normal topic shape complementarity
by holdenj » Fri, 2022-07-15 13:24
1
883 by rmoretti
Fri, 2022-07-15 13:50
Normal topic Error with RNA_denovo
by zmfowler » Thu, 2022-07-14 05:34
0
655 by zmfowler
Thu, 2022-07-14 05:34
Normal topic Error with RoseTTAFold
by sc19 » Thu, 2022-07-14 03:40
0
831 by sc19
Thu, 2022-07-14 03:40
Normal topic Ligand Docking with ROSETTA
by sc19 » Thu, 2022-07-14 01:32
0
765 by sc19
Thu, 2022-07-14 01:34
Normal topic Per residue total score
by johnnytam100 » Wed, 2022-07-13 21:57
0
649 by johnnytam100
Wed, 2022-07-13 21:57
Normal topic SnugDock Partners parameter
by tyang39 » Fri, 2022-07-08 10:02
1
863 by rmoretti
Fri, 2022-07-08 10:27
Normal topic Pepspec - sequence sampling
by almeida85 » Thu, 2022-06-23 04:05
0
682 by almeida85
Thu, 2022-06-23 05:50
Normal topic Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.
by daniloboskovic » Fri, 2019-11-08 08:24
1
2,963 by Payne
Tue, 2022-06-21 07:25
Normal topic Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations
by yliang20 » Wed, 2022-06-15 11:26
2
1,270 by yliang20
Wed, 2022-06-15 13:46
Normal topic Segmentation Fault in Rosetta CM Hybridize
by yliang20 » Mon, 2022-06-06 17:25
2
1,225 by yliang20
Tue, 2022-06-07 08:36
Normal topic Local docking- should I use KIC?
by seayoung lee » Fri, 2022-05-27 02:45
0
789 by seayoung lee
Fri, 2022-05-27 02:45
Normal topic Params for a stapled helix peptide
by e3lm » Thu, 2022-05-26 12:55
0
764 by e3lm
Thu, 2022-05-26 12:55
Normal topic Noncanonical amino acids
by wsgosal » Tue, 2014-03-18 05:29
8
7,092 by e3lm
Thu, 2022-05-26 12:51
Normal topic IL-2 gets better binding with beta / gamma
by tonycheng1688 » Wed, 2022-05-25 10:23
0
780 by tonycheng1688
Wed, 2022-05-25 10:23
Normal topic Relax evaluates protein-DNA complexes?
by pablogalazdavison » Thu, 2022-05-12 12:05
2
1,272 by pablogalazdavison
Fri, 2022-05-20 12:27
Normal topic Enzyme Design Not Editing Structure
by liuwenxi » Wed, 2022-05-18 10:12
0
770 by liuwenxi
Wed, 2022-05-18 10:12

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