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Rosetta 3 - Applications

Topic / Topic starter Repliessort descending Views Last post
Normal topic Can only relax one structure at a time
by lah435 » Wed, 2012-12-12 01:55 		3
 4,100 by smlewis
Mon, 2014-04-21 06:47
Normal topic NCAA attached at two points
by tsztain » Wed, 2021-06-16 15:20 		3
 1,996 by matteoferla
Sat, 2021-06-19 03:07
Normal topic FlexPepDock for protein containing multiple chains
by Dimitrov » Mon, 2012-10-08 08:31 		3
 4,157 by smlewis
Mon, 2014-04-21 06:47
Normal topic Simple comparative modeling (threading) example is failing with "unknown atom name: CA CB"
by brspurri » Fri, 2017-03-24 10:52 		3
 3,952 by brspurri
Fri, 2017-03-24 11:35
Normal topic protein protein interaction design
by Negarsardar » Wed, 2019-05-15 06:13 		3
 3,789 by ajasja
Wed, 2019-05-15 15:40
Normal topic pmut_scan does not produce log file
by fglaser » Wed, 2013-10-16 07:25 		3
 4,569 by matteoferla
Tue, 2018-10-30 02:54
Normal topic No Space
by jrcf » Mon, 2016-01-11 16:18 		3
 3,641 by jrcf
Fri, 2016-02-12 16:42
Normal topic error with fragment_picker.linuxgccrelease
by jiongzhang » Tue, 2012-04-17 09:07 		3
 3,714 by smlewis
Mon, 2014-04-21 06:47
Normal topic building a protein-dna homology model via cm_rosetta
by y_atsmonraz » Wed, 2021-10-20 23:11 		4
 2,292 by y_atsmonraz
Tue, 2021-11-02 01:47
Normal topic minirosetta: weird behavior
by fred » Wed, 2014-01-22 05:57 		4
 5,292 by fred
Mon, 2014-04-21 06:48
Normal topic Specifying resfile in rosetta scripts
by johnnytam100 » Mon, 2019-03-18 02:19 		4
 4,195 by rmoretti
Fri, 2019-03-29 09:30
Normal topic rosetta3.4 fragment file problem
by David Hoover » Wed, 2012-05-16 14:42 		4
 4,408 by dgront
Mon, 2014-04-21 06:47
Normal topic Unable to understand fragment picking tutorial points.
by Danielsebas » Thu, 2019-09-05 03:44 		4
 3,261 by danpf
Fri, 2019-09-06 11:29
Normal topic Relaxed proteins show higher clash score in molprobity results.
by Wang Zhe » Fri, 2021-12-03 04:32 		4
 3,406 by smlewis
Wed, 2021-12-08 13:02
Normal topic RNA structure prediction
by emaghdam » Sat, 2014-02-08 01:30 		4
 6,066 by rmoretti
Mon, 2014-02-24 09:12
Normal topic How to specify only design surface residues and loops by RosettaScripts?
by johnnytam100 » Sun, 2019-04-07 21:47 		4
 3,353 by johnnytam100
Wed, 2019-04-10 02:48
Normal topic ligand_docking_analysis
by Prasanth Kumar » Thu, 2013-05-09 23:51 		4
 5,250 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Changing scoring function for fixbb protocol
by mdyini » Sat, 2012-07-07 18:43 		4
 4,440 by mdyini
Mon, 2014-04-21 06:47
Normal topic Docking Prepack protocol working or not ?
by MJG » Mon, 2017-04-03 08:02 		4
 4,218 by MJG
Tue, 2017-04-04 23:59
Normal topic comparative modelling and broker
by felipet » Tue, 2013-02-05 08:33 		4
 4,505 by smlewis
Mon, 2014-04-21 06:47
Normal topic Antibody modeling
by Maryam_tabasinezhad » Fri, 2015-09-04 11:00 		4
 5,172 by rmoretti
Wed, 2015-09-09 12:08
Normal topic flexpep docking problem-----How to do with phosphorylation peptide?
by MajorID » Thu, 2011-06-02 00:37 		4
 6,512 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Prevention of the negatively charged Nitrogen protonation by coupled_moves
by Corvin » Wed, 2020-11-18 02:56 		4
 2,802 by Corvin
Wed, 2020-11-25 02:58
Normal topic fixbb with symmetry error
by Prasanth Kumar » Sun, 2014-01-26 10:56 		4
 5,668 by Prasanth Kumar
Mon, 2014-04-21 06:48
Normal topic fixbb algorithm reference?
by tylerborrman » Wed, 2015-09-23 10:20 		4
 5,510 by tylerborrman
Mon, 2015-09-28 09:30
Normal topic favor native residue in fixBB design
by ast » Mon, 2012-12-10 06:00 		4
 4,986 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop modelling before peptide docking
by wsgosal » Tue, 2013-10-01 07:24 		4
 5,451 by wsgosal
Mon, 2014-04-21 06:48
Normal topic Options "-out:prefix" didn't work
by maruhuang » Tue, 2019-09-10 05:42 		4
 3,026 by danpf
Fri, 2020-02-21 18:32
Normal topic Error with -patch_selectors
by subha » Tue, 2017-06-06 14:40 		4
 3,950 by subha
Fri, 2017-06-09 15:42
Normal topic Error about rifdocking step 15
by ng98 » Sun, 2024-01-21 16:30 		4
 725 by ng98
Tue, 2024-01-23 17:01
Normal topic Segmentation Fault during prepacking
by Sunyp_IM » Fri, 2020-06-12 11:24 		4
 3,494 by Sunyp_IM
Thu, 2020-07-09 18:40
Normal topic Single Strand DNA (ssDNA) 3D structure prediction
by mkoohim » Fri, 2012-04-06 00:52 		4
 14,900 by smlewis
Mon, 2014-04-21 06:47
Normal topic fa_plane enregy term in scoring weights
by ytao » Fri, 2012-11-30 20:25 		4
 5,210 by smlewis
Mon, 2014-04-21 06:47
Normal topic Relax with protein+complex
by Prasanth Kumar » Wed, 2013-05-08 23:16 		4
 6,013 by Prasanth Kumar
Mon, 2014-04-21 06:47
Normal topic "OSError: [Errno 2]” in “clustering.py”
by lanselibai » Sat, 2014-10-11 14:30 		4
 7,635 by lanselibai
Fri, 2014-10-17 05:10
Normal topic Clustering issue
by Loki01 » Thu, 2018-03-29 10:16 		4
 3,583 by Loki01
Thu, 2018-04-12 08:28
Normal topic ligand_docking tutorial help: do crystal_complex.pdb files need to be prepped before using with <InterfaceScoreCalculator>
by DGR95 » Fri, 2021-04-16 19:26 		4
 2,525 by DGR95
Wed, 2021-04-28 16:13
Normal topic Template/Input length mismatch error during RosettaCM
by marinok » Mon, 2020-05-04 13:12 		4
 2,940 by marinok
Mon, 2020-05-11 12:48
Normal topic Error while running RosettaLigand
by Ryhon Wang » Tue, 2013-07-30 02:51 		4
 5,277 by Ryhon Wang
Mon, 2014-04-21 06:48
Normal topic Abinitio.relax problem on centos
by krlitros87 » Wed, 2014-09-24 11:27 		4
 6,013 by jadolfbr
Tue, 2014-10-07 16:05
Normal topic Backrub Params Files
by protos_heis » Tue, 2012-09-18 06:15 		4
 5,381 by protos_heis
Mon, 2014-04-21 06:47
Normal topic ReplicaDock2.0 demo fails with MPIFileBufJobDistributor: (1) [ ERROR ]
by erpannec » Tue, 2022-08-09 05:42 		4
 2,210 by erpannec
Thu, 2022-09-15 05:17
Normal topic RosettaDesign error with Option file open failed
by xingqing326 » Sun, 2020-04-19 01:56 		4
 4,259 by xingqing326
Tue, 2020-04-21 19:11
Normal topic ddg with ligands
by bhaines1 » Mon, 2011-12-05 14:32 		4
 5,850 by rmoretti
Mon, 2014-04-21 06:47
Normal topic extract_pdbs fails to open silent file when -auto_setup_metals enabled
by attesor » Thu, 2015-01-15 03:22 		4
 5,203 by attesor
Tue, 2015-01-27 02:20
Normal topic Score Functions for Ligand-protein Docking
by ziruiw » Sun, 2021-04-25 13:41 		4
 3,518 by ziruiw
Fri, 2021-04-30 12:01
Normal topic Rebuilding the structure from unknown residues
by sushreet » Mon, 2016-06-27 09:32 		4
 5,498 by rmoretti
Tue, 2016-07-12 09:35
Normal topic fixbb and ncaa's
by jarek » Thu, 2012-11-08 04:55 		4
 5,152 by jcminerlanl
Thu, 2017-12-21 10:13
Normal topic rosetta backrub
by ladimafakher » Thu, 2018-10-04 08:01 		4
 3,648 by ladimafakher
Thu, 2018-11-01 03:47
Normal topic SymDock for docking only the ligand?
by ast » Mon, 2013-06-17 09:53 		4
 5,626 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Docking to TM protein plus lipid bilayer
by renedominik » Tue, 2019-03-12 06:58 		4
 3,968 by elpipasp
Thu, 2023-10-19 04:37
Normal topic Problem readin .ccp4 map file
by jljbbc » Tue, 2011-05-03 11:29 		4
 5,984 by jljbbc
Mon, 2014-04-21 06:47
Normal topic null mutation with ddg_monomer
by fred » Fri, 2012-05-11 07:16 		4
 4,412 by fred
Mon, 2014-04-21 06:47
Normal topic How to estimate the effect of a mutation on the binding energy?
by ltrabuco » Tue, 2011-02-15 08:02 		4
 5,699 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Segmentation Fault
by ajaniharesh » Fri, 2019-03-29 11:21 		4
 6,501 by ajaniharesh
Thu, 2019-04-04 07:07
Normal topic Coverage of sequence space?
by johnnytam100 » Sun, 2019-04-21 23:25 		4
 3,841 by johnnytam100
Thu, 2019-04-25 19:28
Normal topic Thread target sequence
by duz » Thu, 2021-04-01 10:09 		4
 2,433 by duz
Mon, 2021-05-03 07:50
Normal topic Sequence design with mixed fixbb-relax protocol
by kszczepaniak » Thu, 2013-10-03 08:11 		4
 5,848 by fede
Wed, 2020-09-23 11:24
Normal topic Warning messages in Interface analyzer output
by Pernille » Wed, 2015-03-25 00:53 		4
 4,757 by rmoretti
Tue, 2015-03-31 08:20
Normal topic Error while running "make_fragments.pl".....[blastpgp] ERROR: Arguments must start with '-'
by AG88 » Thu, 2011-11-03 01:25 		4
 7,903 by weitzner
Mon, 2014-04-21 06:47
Normal topic select_best_unique_ligand_poses - Ligand docking
by subha » Thu, 2018-04-19 10:36 		4
 3,496 by subha
Fri, 2018-04-20 12:49
Normal topic antibody_numbering_converter cannot recognize the IMGT scheme
by cryosky » Sat, 2020-02-29 23:12 		4
 3,234 by jadolfbr
Sun, 2020-03-01 14:54
Normal topic Error when running Remodel with EnzDes constraint file to extend c-terminal
by Jeffrey_Chen » Thu, 2017-01-19 06:20 		4
 4,533 by dfcoelho
Tue, 2017-10-17 11:52
Normal topic Error while reading in silent file
by rweisse » Mon, 2015-04-20 00:31 		4
 5,773 by rmoretti
Thu, 2015-04-30 16:46
Normal topic conformational sampling of multi domain protein
by dhirajks » Tue, 2017-07-04 11:20 		4
 3,963 by jrporter
Wed, 2017-07-05 06:30
Normal topic Re: Glutamic acid protonation
by bharat_46010 » Fri, 2017-02-10 03:08 		4
 4,995 by rmoretti
Mon, 2017-02-20 08:09
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49 		4
 4,721 by sacch
Mon, 2014-04-21 06:47
Normal topic Problem passing a list of PDB files to minimize_with_cst
by dolevrahat » Sun, 2018-11-18 16:13 		4
 2,031 by rmoretti
Thu, 2024-06-20 11:44
Normal topic homology modelling with DNA
by zadie1118 » Fri, 2012-09-28 06:35 		4
 5,968 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Positive scores with SymmDock in helical symmetry
by kxiao » Tue, 2014-02-11 07:37 		4
 4,843 by kxiao
Thu, 2014-06-05 08:37
Normal topic mr_protocols with symmetry and ligand
by jhm13c » Mon, 2017-02-27 11:59 		4
 3,979 by jhm13c
Thu, 2017-03-02 12:01
Normal topic When using "screening job files" in small molecule-docking I get: Residue type already exists in the cache Error
by Martin Floor » Thu, 2020-09-17 06:01 		4
 2,998 by Martin Floor
Tue, 2020-09-22 00:48
Normal topic Pepspec Errors running 3.4
by rrphenix » Tue, 2013-05-28 12:08 		4
 4,576 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ddg_monomer: what is the meaning of "total score" and "score"?
by lanselibai » Tue, 2015-01-13 14:49 		4
 7,042 by rmoretti
Thu, 2015-04-16 11:23
Normal topic RosettaAntibody3 is failing with "Error: no input sequences were specified!"
by brspurri » Sun, 2020-08-16 16:16 		4
 2,957 by brspurri
Tue, 2020-08-18 09:57
Normal topic Multiple ligands in enzyme design application
by yogeshkd » Mon, 2013-02-11 10:13 		4
 5,509 by yogeshkd
Mon, 2014-04-21 06:47
Normal topic Dimer of dimers
by smiruthi » Fri, 2011-04-15 10:41 		4
 7,309 by IAndre
Mon, 2014-04-21 06:47
Normal topic relax protein with multi-conformer bound ligand
by xfradera » Thu, 2023-01-12 09:10 		4
 3,676 by rmoretti
Mon, 2023-02-06 15:06
Normal topic ddg_monomer and membrane proteins
by afmo » Tue, 2014-05-20 02:37 		4
 5,915 by afmo
Thu, 2014-05-22 01:19
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
 1,933 by almeida85
Thu, 2022-08-11 00:58
Normal topic side chain repacking error
by malkeet.singh » Thu, 2017-12-07 04:49 		4
 4,331 by smlewis
Wed, 2017-12-13 09:54
Normal topic Any backrub expert?
by johnnytam100 » Fri, 2019-03-01 01:58 		4
 3,778 by johnnytam100
Sun, 2019-03-03 23:42
Normal topic Rosetta antibody- modeling in the presense of an antigen
by agctomer » Mon, 2021-02-01 03:19 		4
 2,304 by nannemdp
Wed, 2021-02-03 08:52
Normal topic ddg_monomer: How the ddG is actually calculated based on the 50 trajectories? What scorefunction is used?
by lanselibai » Tue, 2015-02-24 02:38 		4
 6,548 by lanselibai
Sun, 2015-03-01 15:00
Normal topic make_rot_lib issue
by jarek » Thu, 2013-04-11 08:21 		4
 5,118 by smlewis
Mon, 2014-04-21 06:47
Normal topic "Problem in calculating overlap between atoms" error occurred in Point Mutant Scan application
by xfliu » Thu, 2012-06-21 09:07 		4
 5,323 by smlewis
Mon, 2014-04-21 06:47
Normal topic rosetta.script segmentation fault
by felipet » Wed, 2013-10-02 10:41 		4
 6,286 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic How to run simulations with non-canonical amino acids?
by Denise » Thu, 2017-06-08 07:50 		4
 4,340 by Denise
Thu, 2017-06-15 04:26
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40 		4
 5,101 by cossio
Mon, 2015-01-19 07:10
Normal topic RosettaCM: An internal error has occurred when "Running the Hybridize mover"
by haom » Mon, 2020-06-15 05:56 		4
 2,636 by haom
Tue, 2020-06-16 05:55
Normal topic Filter for fixed-bb design using RosettaScript?
by chrisHKL » Fri, 2020-02-28 19:47 		4
 2,729 by vmulligan
Mon, 2020-03-02 13:40
Normal topic Can I assume the outputs from different runs are from a same batch?
by lanselibai » Mon, 2014-11-03 06:34 		4
 4,926 by lanselibai
Mon, 2014-11-03 13:15
Normal topic antibody.linuxgccrelease- output models don't have the same sequence as the input fasta
by agctomer » Thu, 2021-01-21 15:35 		4
 2,484 by agctomer
Sun, 2021-01-31 01:06
Normal topic Structure prediction using true distance and angle constraint
by maruhuang » Wed, 2019-08-21 02:29 		4
 2,756 by maruhuang
Thu, 2019-09-26 18:52
Normal topic Ligand Docking with Rosetta Scripts memory problem
by Swillard » Thu, 2017-08-17 14:59 		5
 5,123 by rmoretti
Mon, 2018-11-12 14:31
Normal topic RosettaCM -weights, fragments and relax
by jsv » Tue, 2017-05-09 10:20 		5
 5,256 by rmoretti
Thu, 2017-06-01 08:52
Normal topic Cartesian-space refinement
by sjyang7 » Wed, 2017-05-31 19:34 		5
 5,941 by sjyang7
Sat, 2017-06-03 06:09
Normal topic cyclization_type flag in simple_cycpep_predict
by Florent Langenfeld » Thu, 2018-01-04 09:22 		5
 4,968 by Florent Langenfeld
Tue, 2018-03-27 11:44
Normal topic RosettaLigand: How to score native pose in protein-ligand docking experiment?
by Ryhon Wang » Tue, 2015-11-10 01:30 		5
 6,022 by Ryhon Wang
Mon, 2016-01-04 19:59
Normal topic Rosetta ScriptsFeatures Reporter issue
by David Weis » Sun, 2017-03-12 08:19 		5
 4,935 by David Weis
Mon, 2017-03-13 10:59