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Rosetta 3 - Applications

Topic / Topic starter Repliessort ascending Views Last post
Normal topic Disulfide Bonds in Loop Modeling
by code_Monkey » Mon, 2021-05-03 08:27 		2
 1,776 by code_Monkey
Thu, 2021-05-06 07:14
Normal topic Reproducing the exact result using information from previos run
by nawsad » Thu, 2013-03-14 12:05 		2
 2,750 by nawsad
Mon, 2014-04-21 06:47
Normal topic FlexPepDock and total score problem
by tkellici » Fri, 2014-01-17 06:07 		2
 3,389 by Ora Schueler-Furman
Mon, 2014-04-21 06:48
Normal topic OptimizeMembranePositionMover - This element is not expected
by bjharris » Wed, 2020-07-01 23:21 		2
 2,040 by bjharris
Thu, 2020-07-02 11:09
Normal topic How do I change the default Compiler for Rosetta？
by pagumaaaaa » Wed, 2022-03-16 00:23 		2
 1,676 by pagumaaaaa
Thu, 2022-03-24 22:40
Normal topic homology modeling- Error: length mismatch between sequence and alignment.
by pdbb » Mon, 2012-10-01 07:57 		2
 4,578 by pdbb
Mon, 2014-04-21 06:47
Normal topic -loops:fa_input not found in command line top-level context
by swarekwood » Thu, 2017-08-24 03:15 		2
 2,759 by swarekwood
Fri, 2017-08-25 05:08
Normal topic ligand docking with MPI
by Ruska322 » Wed, 2019-09-04 03:47 		2
 1,901 by Ruska322
Fri, 2019-09-06 07:13
Normal topic ligand_docking ligand preparation
by Alison_Yajie » Thu, 2020-05-21 10:21 		2
 1,747 by Alison_Yajie
Wed, 2020-06-24 12:38
Normal topic Fastrelax problem
by Pernille » Fri, 2014-06-20 00:16 		2
 4,091 by Pernille
Thu, 2014-07-03 07:21
Normal topic Filter ddg_filter reports failure!
by deepanshuiitb » Fri, 2015-02-27 18:19 		2
 3,165 by deepanshuiitb
Sat, 2015-02-28 19:24
Normal topic very good I_sc values (if not too good)
by attesor » Tue, 2015-11-03 03:30 		2
 3,357 by attesor
Tue, 2015-11-17 07:36
Normal topic Ensemble docking causes segmentation fault 11
by David Weis » Mon, 2017-03-06 14:30 		2
 3,100 by David Weis
Mon, 2017-03-13 06:40
Normal topic Centroid mode minimization
by Martin Floor » Tue, 2020-01-21 07:34 		2
 2,154 by Martin Floor
Tue, 2020-01-21 11:15
Normal topic remove membrane for RosettaMPdock
by lluoto » Wed, 2023-12-06 06:22 		2
 681 by lluoto
Wed, 2024-02-21 17:39
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59 		2
 3,354 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic residues_patch_selectors CENTROID_HA
by Pernille » Fri, 2014-10-03 03:53 		2
 3,156 by Pernille
Wed, 2014-10-08 10:41
Normal topic docking with constraints and flexible bb
by mintseris » Mon, 2015-06-22 09:07 		2
 3,265 by mintseris
Wed, 2015-06-24 22:04
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05 		2
 2,243 by dnamkr
Fri, 2022-04-22 17:00
Normal topic high-res docking
by tfliu » Mon, 2013-07-15 02:49 		2
 3,440 by tfliu
Mon, 2014-04-21 06:48
Normal topic error extracting PDB from silent from AbinitioRelax with constraints
by attesor » Wed, 2017-06-14 04:15 		2
 2,490 by smlewis
Fri, 2017-06-16 07:35
Normal topic Docking with constraint
by Hongtham » Sat, 2014-12-27 09:56 		2
 2,957 by rmoretti
Fri, 2015-01-02 09:43
Normal topic Docking-I_sc values do not correlate
by jlawrie » Wed, 2020-08-12 08:08 		2
 1,882 by jlawrie
Wed, 2020-08-12 08:57
Normal topic minimize_with_cst problems (ddg_monomer)
by alexn » Tue, 2011-09-20 13:46 		2
 3,720 by alexn
Mon, 2014-04-21 06:47
Normal topic membrane score weights
by ytao » Sat, 2012-09-08 06:56 		2
 3,104 by ytao
Mon, 2014-04-21 06:47
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Tue, 2011-02-15 17:23 		2
 3,633 by sumukh21
Mon, 2014-04-21 06:47
Normal topic How do I explicitly add residues for design in the interface optimization script?
by ahonegger » Mon, 2014-05-12 07:40 		2
 3,589 by ahonegger
Mon, 2014-05-12 09:08
Normal topic AddHelixSequenceConstraints Mover
by Negarsardar » Thu, 2019-05-30 03:17 		2
 1,970 by vmulligan
Thu, 2019-06-13 14:59
Normal topic InterfaceAnalyzer dSasa calculation
by mintseris » Wed, 2015-09-02 09:43 		2
 4,653 by jadolfbr
Thu, 2015-09-03 16:18
Normal topic How to correctly incorporate constraint information into ab initio structure prediction?
by johnnytam100 » Tue, 2019-02-19 03:13 		2
 2,391 by johnnytam100
Fri, 2019-03-01 01:36
Normal topic Structure determination combining X-ray diffraction data and NMR chemical shift
by MajorID » Mon, 2011-10-17 19:55 		2
 3,968 by rmoretti
Mon, 2014-04-21 06:47
Normal topic not knowing which one of three ways to run rosettascript
by xinmiaohe » Tue, 2020-10-13 13:52 		2
 2,259 by xinmiaohe
Mon, 2020-10-19 13:18
Normal topic Ligand atom RMSD calculation
by lkrathn » Wed, 2013-08-14 21:25 		2
 4,826 by lkrathn
Mon, 2014-04-21 06:48
Normal topic Warnings during relax
by cossio » Thu, 2018-10-11 14:42 		2
 3,641 by rmoretti
Mon, 2019-11-04 13:56
Normal topic Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1
by cm21 » Wed, 2020-05-20 08:55 		2
 1,916 by cm21
Wed, 2020-05-20 11:22
Normal topic The energy terms in InterfaceAnalyzer
by Sunyp_IM » Tue, 2021-11-02 18:43 		2
 1,608 by zivben
Sat, 2021-11-13 04:49
Normal topic how to reconstruct the whole complex after symmetric docking
by Anonymous » Tue, 2012-07-03 02:44 		2
 3,392 by felipet
Wed, 2014-07-02 07:26
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46 		2
 4,735 by libai2098
Mon, 2014-04-21 06:47
Normal topic Problems with fixbb in Rosetta 3.5
by mdidonato » Wed, 2014-06-04 13:56 		2
 2,809 by mdidonato
Wed, 2014-06-04 14:55
Normal topic Scoring docking error
by almeida85 » Wed, 2020-09-02 01:32 		2
 1,788 by almeida85
Wed, 2020-09-02 06:14
Normal topic Abinito for Multimers
by Prasanth Kumar » Wed, 2014-01-22 17:45 		2
 3,623 by Prasanth Kumar
Mon, 2014-04-21 06:48
Normal topic Not found some Flags
by jrcf » Sat, 2015-09-19 12:08 		2
 4,191 by jrcf
Mon, 2015-09-21 11:10
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
 762 by lei
Wed, 2023-09-13 19:35
Normal topic limit_cluster_size default value
by sacch » Thu, 2011-11-24 17:57 		2
 3,062 by sacch
Mon, 2014-04-21 06:47
Normal topic Problem with SymmDock in helical symmetry
by mumdonar » Wed, 2013-09-18 03:59 		2
 3,969 by mumdonar
Mon, 2014-04-21 06:48
Normal topic where is generate_ligens.linuxgccrelease?
by Nicole Deng » Thu, 2020-12-03 00:00 		2
 1,913 by Nicole Deng
Fri, 2020-12-18 00:28
Normal topic printing our per-residue energies including H-bonding energies
by vijayan » Tue, 2013-07-02 08:51 		2
 3,853 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Adding water interactions when docking a ligand with Rosetta 3.7.
by brspurri » Thu, 2017-06-01 09:37 		2
 3,595 by brspurri
Thu, 2017-06-01 10:58
Normal topic Modeling flexible linkers with Floppytail
by pdbb » Sun, 2013-05-12 15:55 		2
 3,397 by smlewis
Mon, 2014-04-21 06:47
Normal topic Docking seems to not parse the -nstruct flag
by rosend » Tue, 2015-11-17 12:01 		2
 3,949 by rosend
Tue, 2015-11-17 12:12
Normal topic DDG_monomer application
by shadrinams » Mon, 2018-02-12 12:14 		2
 3,473 by shadrinams
Wed, 2018-03-14 07:46
Normal topic Error when trying docking protocol with different ligand
by scyphs » Wed, 2020-08-05 04:37 		2
 1,695 by scyphs
Mon, 2020-08-10 08:09
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
 1,759 by yliang20
Wed, 2022-06-15 13:46
Normal topic protein-ligand docking rescoring with interfaceAnalyzer
by syntekabio2019 » Sat, 2020-12-19 03:59 		2
 1,565 by syntekabio2019
Sun, 2020-12-20 21:10
Normal topic Pepspec - random runtime segfaults (rosetta 3.3 database replaced) [solved]
by loreseeker » Wed, 2011-09-14 08:13 		2
 3,784 by loreseeker
Mon, 2014-04-21 06:47
Normal topic D-amino acids tripeptide docking.
by sam_dc » Sat, 2021-07-03 08:48 		2
 1,650 by vmulligan
Tue, 2021-07-06 08:27
Normal topic flexpep docking, select the decoy to do the further docking, questions
by michael_luntan » Fri, 2011-04-22 04:43 		2
 3,653 by michael_luntan
Mon, 2014-04-21 06:47
Normal topic Element 'trRosettaProtocol': This element is not expected.
by csaylan » Tue, 2021-04-20 14:21 		2
 1,617 by csaylan
Tue, 2021-04-20 16:13
Normal topic How to debug the XML script file?
by intomybioverse » Wed, 2024-03-06 06:32 		2
 407 by rmoretti
Wed, 2024-03-06 06:51
Normal topic homology modeling with threading says length mismatch between sequence and alignment
by rqliang » Thu, 2015-08-06 11:46 		2
 3,027 by jharamesh
Sat, 2015-08-08 19:51
Normal topic The Usage of motifgraft
by Sunyp_IM » Sun, 2017-11-19 20:22 		2
 3,602 by Sunyp_IM
Mon, 2017-11-20 19:20
Normal topic Chemically bound ligand connection error
by tsztain » Tue, 2019-01-01 18:40 		2
 2,462 by tsztain
Mon, 2019-02-18 09:55
Normal topic Speed problem when running RosettaLigand ligand docking
by Nicole Deng » Tue, 2019-10-08 04:29 		2
 2,355 by Nicole Deng
Tue, 2020-11-03 19:07
Normal topic PyIgClassify cannot renumber and label CDRs my Nanobody-Antigen complex for RabD
by WBNeT » Fri, 2023-07-07 10:58 		2
 819 by josiefanxu
Tue, 2024-05-14 21:17
Normal topic flexpepdock_score_only
by ays » Sun, 2014-09-21 06:17 		2
 2,803 by ays
Tue, 2014-09-30 08:31
Normal topic SPLINE EPR_DISTANCE Constraint Error
by mmw88 » Tue, 2018-09-18 14:39 		2
 2,569 by rmoretti
Thu, 2018-09-20 09:19
Normal topic RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?
by brspurri » Thu, 2020-05-14 11:15 		2
 1,766 by brspurri
Thu, 2020-05-14 12:24
Normal topic A question on the logic of enzyme design
by agulsevin » Thu, 2013-06-13 08:10 		2
 4,179 by agulsevin
Mon, 2014-04-21 06:48
Normal topic How to use rewrite_rosetta_script.py to update XML script file?
by intomybioverse » Fri, 2024-03-15 06:44 		2
 368 by intomybioverse
Sun, 2024-03-17 06:22
Normal topic Packstat score in InterfaceAnalyzer
by Vedasheersh » Fri, 2017-01-27 06:21 		2
 3,263 by smlewis
Fri, 2017-01-27 07:20
Normal topic Alanine Scanning for 1 Protein (no interface)
by mags33 » Fri, 2019-10-25 10:08 		2
 2,548 by mags33
Wed, 2019-11-06 09:35
Normal topic Rosetta Design: Non-canonical amino acid substrate not accepted
by Friedrich Ehinger » Fri, 2023-08-04 00:09 		2
 780 by Friedrich Ehinger
Fri, 2023-08-04 08:38
Normal topic How to sort a Silent File based on RMSD
by JadAbbass » Sun, 2013-08-04 14:40 		2
 3,698 by lanselibai
Mon, 2014-10-06 15:30
Normal topic cluster.mpi running in MPI mode?
by sacch » Fri, 2011-11-18 23:30 		2
 4,576 by sacch
Mon, 2014-04-21 06:47
Normal topic Error: in membrane docking : Cannot split pose by membrane jump! Quitting...
by Astghik » Tue, 2020-11-24 05:27 		2
 1,761 by Astghik
Thu, 2020-12-03 02:35
Normal topic ligand_docking
by yang » Thu, 2023-02-16 04:37 		2
 2,663 by yang
Wed, 2023-02-22 19:18
Normal topic Floppytail modelling
by felipet » Fri, 2011-06-24 09:23 		2
 3,906 by felipet
Mon, 2014-04-21 06:47
Normal topic RosettaSurface in 3.4?
by skovacs » Tue, 2012-07-10 16:02 		2
 3,151 by mpacella
Mon, 2014-04-21 06:47
Normal topic CSrosetta run problem
by erin_cutts » Fri, 2013-06-28 09:52 		2
 3,822 by erin_cutts
Mon, 2014-04-21 06:48
Normal topic ddG Monomer Low Res Protocol Convergence
by harshkhare » Thu, 2012-03-01 00:45 		2
 3,962 by harshkhare
Mon, 2014-04-21 06:47
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26 		2
 4,741 by tingting
Tue, 2022-03-15 23:55
Normal topic Rosetta_cm Segmentation Fault
by gszwabowski » Thu, 2019-06-20 12:55 		2
 2,585 by gszwabowski
Wed, 2019-06-26 10:25
Normal topic cartfrag_overlap error while running hybridize protocol
by sn » Thu, 2017-12-21 10:24 		2
 2,375 by dnamkr
Mon, 2019-12-30 11:43
Normal topic Rosetta Script for ddg_monomer protocol 16
by cossio » Thu, 2018-01-25 08:23 		2
 2,788 by cossio
Sun, 2018-03-11 09:12
Normal topic Protein Ensemble RosettaLigand Docking
by sam_dc » Fri, 2021-03-26 10:18 		2
 1,656 by sam_dc
Fri, 2021-03-26 12:04
Normal topic relax constraints not minimized
by m_grisewood » Fri, 2012-08-10 08:31 		2
 3,861 by m_grisewood
Mon, 2014-04-21 06:47
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03 		2
 2,000 by jlawrie
Wed, 2020-08-12 07:27
Normal topic r_frag_quality
by ii_cnr » Mon, 2021-04-12 03:06 		2
 1,582 by ii_cnr
Mon, 2021-04-12 23:44
Normal topic Flexpep docking freezing issue at "press enter to continue"
by rlwoltz » Tue, 2013-01-22 13:31 		2
 3,257 by rlwoltz
Mon, 2014-04-21 06:47
Normal topic ab initio modelling - what to do next?
by krlitros87 » Thu, 2014-10-16 13:05 		2
 3,515 by krlitros87
Wed, 2014-10-22 09:31
Normal topic score:weights for fixbb application in Rosetta 3.5
by tylerborrman » Tue, 2015-07-28 14:16 		2
 2,941 by tylerborrman
Wed, 2015-09-23 10:51
Normal topic Altering substrate specificity
by bp » Thu, 2016-12-22 02:45 		2
 2,832 by bp
Thu, 2016-12-22 07:54
Normal topic Model monomer to fit cryo density map of a filament
by BuddySphinx » Wed, 2018-12-12 18:58 		2
 2,229 by BuddySphinx
Sun, 2018-12-30 16:49
Normal topic BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?
by daniloboskovic » Wed, 2020-04-29 01:17 		2
 1,922 by daniloboskovic
Wed, 2020-04-29 05:51
Normal topic How to add a residue to one chain of an existing structure?
by sn » Mon, 2017-04-17 09:34 		2
 3,543 by sn
Thu, 2017-04-20 21:43
Normal topic protein interface design
by Negarsardar » Tue, 2019-05-28 07:04 		2
 2,286 by Negarsardar
Thu, 2019-05-30 23:46
Normal topic Successful RosettaCM?
by jlawrie » Wed, 2020-08-19 06:53 		2
 1,910 by jlawrie
Thu, 2020-08-20 11:00
Normal topic Filling the missing loops
by code_Monkey » Tue, 2021-04-27 07:44 		2
 1,883 by code_Monkey
Tue, 2021-04-27 12:11
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
 755 by ramon-arg
Fri, 2023-07-14 07:47
Normal topic Enzdes scorefile lost, can I recreate it
by eyong123 » Wed, 2015-04-15 05:55 		2
 2,842 by eyong123
Wed, 2015-04-22 11:33