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Rosetta 3 - Applications

Topic / Topic starter Replies Viewssort descending Last post
Normal topic minimize_with_cst problems (ddg_monomer)
by alexn » Tue, 2011-09-20 13:46
2
3,558 by alexn
Mon, 2014-04-21 06:47
Normal topic cartesian_ddg output
by cossio » Thu, 2018-10-11 14:58
2
3,575 by cossio
Fri, 2018-10-12 04:43
Normal topic Total score problems with high-res ddg_monomer
by jklesmith » Tue, 2015-03-10 15:54
2
3,583 by jennifer
Fri, 2015-03-27 05:56
Normal topic Threading a sequence onto a template with ligands/metal ions included
by ajkal » Wed, 2017-04-19 11:53
3
3,591 by ahmadkhalifa
Sun, 2019-03-31 23:27
Normal topic Coverage of sequence space?
by johnnytam100 » Sun, 2019-04-21 23:25
4
3,594 by johnnytam100
Thu, 2019-04-25 19:28
Normal topic example scripts for comparative modeling
by fglaser » Sun, 2011-02-27 21:50
2
3,595 by maxebert
Mon, 2014-04-21 06:47
Normal topic Residue_energy_breakdown utility
by cn » Sat, 2012-03-17 06:11
3
3,596 by cn
Mon, 2014-04-21 06:47
Normal topic Missing atoms and cannot find atom pose when refining ligand position with EM density
by BuddySphinx » Mon, 2018-12-31 16:22
2
3,605 by e3lm
Tue, 2021-09-14 10:02
Normal topic De novo model-building guided by exprimental density data
by dee2711453 » Thu, 2016-03-10 17:28
3
3,605 by dee2711453
Fri, 2016-03-11 21:32
Normal topic MaxSub and MaxSub2.0
by JadAbbass » Tue, 2013-10-15 13:36
2
3,621 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic RosettaRemodel
by gw » Wed, 2011-09-14 13:24
2
3,624 by smlewis
Mon, 2014-04-21 06:47
Normal topic Add missing residues in loop modeling
by exchhattu » Thu, 2013-06-20 17:38
1
3,630 by smlewis
Mon, 2014-04-21 06:48
Normal topic Does relax.linuxgccrelease fully relax the structure compared to ddg_monomer.linuxgccrelease?
by lanselibai » Thu, 2015-01-08 03:23
3
3,634 by lanselibai
Tue, 2015-01-13 14:25
Normal topic Alanine Scanning
by gjbartlett » Mon, 2013-08-05 07:02
1
3,637 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Pepspec - random runtime segfaults (rosetta 3.3 database replaced) [solved]
by loreseeker » Wed, 2011-09-14 08:13
2
3,646 by loreseeker
Mon, 2014-04-21 06:47
Normal topic scoring input pdbs as the same as docking score
by hamedkhakzad » Fri, 2016-07-01 07:15
3
3,664 by rmoretti
Tue, 2016-07-12 09:05
Normal topic Problem with mpirun/mpiexec
by ahansel » Fri, 2020-07-10 08:37
1
3,677 by rmoretti
Fri, 2020-07-10 09:59
Normal topic Trouble enforcing a disulfide in loop building
by chelsell » Sun, 2015-05-10 16:31
2
3,690 by chelsell
Wed, 2015-05-27 14:36
Normal topic Fnat and Irms are nan in score.sc from docking_protocol?
by cossio » Sun, 2015-09-13 07:34
2
3,695 by rmoretti
Thu, 2015-09-17 12:47
Normal topic Compiling Rosetta 3.3 on Linux Mint
by proteinproteindock » Thu, 2011-09-01 16:05
2
3,704 by proteinproteindock
Mon, 2014-04-21 06:47
Normal topic CSrosetta run problem
by erin_cutts » Fri, 2013-06-28 09:52
2
3,706 by erin_cutts
Mon, 2014-04-21 06:48
Normal topic How to preserve ACE/NME termini?
by nitroamos » Tue, 2018-05-22 13:07
3
3,707 by rmoretti
Thu, 2018-06-28 12:44
Normal topic relax constraints not minimized
by m_grisewood » Fri, 2012-08-10 08:31
2
3,719 by m_grisewood
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
3,723 by brspurri
Fri, 2017-03-24 11:35
Normal topic Error with -patch_selectors
by subha » Tue, 2017-06-06 14:40
4
3,725 by subha
Fri, 2017-06-09 15:42
Normal topic Running RosettaHoles2
by weehee » Wed, 2013-02-13 09:35
3
3,727 by weehee
Mon, 2014-04-21 06:47
Normal topic printing our per-residue energies including H-bonding energies
by vijayan » Tue, 2013-07-02 08:51
2
3,732 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Relax is resulting in a Segmentation Fault
by brspurri » Thu, 2017-08-24 18:46
3
3,740 by brspurri
Sat, 2017-08-26 07:08
Normal topic rotamer library in coupled_moves
by mtyras » Fri, 2015-05-29 07:46
2
3,745 by mtyras
Mon, 2015-06-08 03:18
Normal topic conformational sampling of multi domain protein
by dhirajks » Tue, 2017-07-04 11:20
4
3,748 by jrporter
Wed, 2017-07-05 06:30
Normal topic Floppytail modelling
by felipet » Fri, 2011-06-24 09:23
2
3,748 by felipet
Mon, 2014-04-21 06:47
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37
3
3,752 by rmoretti
Tue, 2017-10-10 09:58
Normal topic Docking seems to not parse the -nstruct flag
by rosend » Tue, 2015-11-17 12:01
2
3,757 by rosend
Tue, 2015-11-17 12:12
Normal topic Extract PDB structures from database
by cossio » Mon, 2018-01-29 09:30
3
3,769 by rmoretti
Fri, 2018-11-23 11:23
Normal topic Multiple Chain Comparative Modeling - End result is not even close to template structure
by eskici » Wed, 2012-08-29 08:09
2
3,769 by eskici
Mon, 2014-04-21 06:47
Normal topic mr_protocols with symmetry and ligand
by jhm13c » Mon, 2017-02-27 11:59
4
3,777 by jhm13c
Thu, 2017-03-02 12:01
Normal topic Error encountered during Rosetta loop modeling
by max » Tue, 2014-11-25 02:17
3
3,788 by max
Thu, 2014-11-27 02:56
Normal topic Structure determination combining X-ray diffraction data and NMR chemical shift
by MajorID » Mon, 2011-10-17 19:55
2
3,804 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Why there are two outputs using pmut_scan_parallel.linuxgccrelease with a mutant list file?
by lanselibai » Sun, 2014-11-16 10:26
3
3,807 by G Mustafa
Thu, 2018-10-18 05:31
Normal topic ddG Monomer Low Res Protocol Convergence
by harshkhare » Thu, 2012-03-01 00:45
2
3,808 by harshkhare
Mon, 2014-04-21 06:47
Normal topic Enzdes constraint file not defined correctly
by eyong123 » Fri, 2015-03-27 07:16
3
3,816 by rmoretti
Thu, 2015-04-16 10:38
Normal topic strange effect in: SymDock.linuxgccrelease
by ast » Tue, 2013-06-11 11:05
3
3,833 by ast
Mon, 2014-04-21 06:48
Normal topic Unable to set up interface foldtree because there are no movable jumps - (antibody/antigen docking)
by snorp » Mon, 2014-04-14 13:01
2
3,841 by jadolfbr
Mon, 2014-05-12 10:41
Normal topic Problem with SymmDock in helical symmetry
by mumdonar » Wed, 2013-09-18 03:59
2
3,845 by mumdonar
Mon, 2014-04-21 06:48
Normal topic ddg_monomer: what is the theoretical solution condition for the scoring?
by lanselibai » Sat, 2016-04-30 03:26
3
3,847 by smlewis
Mon, 2016-05-02 08:20
Normal topic Specifying resfile in rosetta scripts
by johnnytam100 » Mon, 2019-03-18 02:19
4
3,863 by rmoretti
Fri, 2019-03-29 09:30
Normal topic Executing the clean_pdb.py script
by Rkfoury » Fri, 2015-02-20 10:16
1
3,863 by lanselibai
Tue, 2015-02-24 02:36
Normal topic pdb2vall
by JadAbbass » Mon, 2013-07-08 12:11
3
3,879 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Ligand dock analysis
by sacch » Tue, 2012-05-22 01:20
3
3,881 by glemmon
Mon, 2014-04-21 06:47
Normal topic Missing CS-HM-Rosetta Binary files
by Marius1987 » Wed, 2016-02-10 05:52
3
3,884 by Marius1987
Mon, 2016-03-14 04:34
Normal topic Fastrelax problem
by Pernille » Fri, 2014-06-20 00:16
2
3,892 by Pernille
Thu, 2014-07-03 07:21
Normal topic Can't append or prepend with pepspec
by danzinho » Tue, 2015-03-31 01:19
3
3,896 by dswhit
Tue, 2015-04-21 10:14
Normal topic RosettaDesign error with Option file open failed
by xingqing326 » Sun, 2020-04-19 01:56
4
3,898 by xingqing326
Tue, 2020-04-21 19:11
Normal topic Loop design with length variation
by jarod » Thu, 2016-06-16 19:54
3
3,902 by rmoretti
Tue, 2016-07-12 09:41
Normal topic Lammps or RosettaSurface
by StevPChem » Fri, 2016-06-10 10:13
3
3,910 by Anpu
Tue, 2018-09-25 18:53
Normal topic ddG filter gives deltaG calculation number?
by jarod » Tue, 2013-05-28 23:43
2
3,915 by jarod
Mon, 2014-04-21 06:47
Normal topic RosettaCM Ignoring Ligand
by Delfosse57 » Sun, 2022-12-04 12:05
0
3,918 by Delfosse57
Sun, 2022-12-04 12:05
Normal topic Syntax to extract PDB files from a silent file
by lanselibai » Fri, 2014-09-26 13:48
1
3,919 by lanselibai
Fri, 2014-09-26 14:58
Normal topic Can only relax one structure at a time
by lah435 » Wed, 2012-12-12 01:55
3
3,925 by smlewis
Mon, 2014-04-21 06:47
Normal topic High energies after loopmodel run
by michki » Thu, 2014-05-08 05:14
3
3,934 by rmoretti
Mon, 2014-05-12 15:16
Normal topic folding ectodomain in membrane ab initio
by freedman » Mon, 2015-05-25 21:09
3
3,936 by rmoretti
Fri, 2015-06-19 13:53
Normal topic what does initialize_rigid_body_dofs do?
by attesor » Mon, 2015-10-26 05:12
3
3,943 by rmoretti
Tue, 2015-11-10 11:35
Normal topic proline patching problem
by xun » Tue, 2012-01-03 11:15
3
3,956 by xun
Mon, 2014-04-21 06:47
Normal topic Docking Prepack protocol working or not ?
by MJG » Mon, 2017-04-03 08:02
4
3,979 by MJG
Tue, 2017-04-04 23:59
Normal topic  The error of InterfaceAnalyzer
by asbelx » Thu, 2017-12-21 19:04
3
3,993 by smlewis
Sat, 2017-12-23 15:56
Normal topic Error when running Remodel with EnzDes constraint file
by aloshbau » Wed, 2013-04-17 22:23
2
3,997 by aloshbau
Mon, 2014-04-21 06:47
Normal topic FlexPepDock for protein containing multiple chains
by Dimitrov » Mon, 2012-10-08 08:31
3
3,997 by smlewis
Mon, 2014-04-21 06:47
Normal topic side chain repacking error
by malkeet.singh » Thu, 2017-12-07 04:49
4
4,003 by smlewis
Wed, 2017-12-13 09:54
Normal topic Problems running pmut in parallel with openmpi
by RMJ » Fri, 2012-09-21 06:25
2
4,004 by RMJ
Mon, 2014-04-21 06:47
Normal topic rosetta app
by MA » Wed, 2017-07-05 06:52
5
4,006 by smlewis
Tue, 2017-07-11 07:53
Normal topic score_jd2.linuxgccrelease documentation
by fglaser » Mon, 2011-08-01 04:08
1
4,016 by smlewis
Mon, 2014-04-21 06:47
Normal topic A question on the logic of enzyme design
by agulsevin » Thu, 2013-06-13 08:10
2
4,031 by agulsevin
Mon, 2014-04-21 06:48
Normal topic Modeling of side-chains onto membrane ab initio cluster?
by akfried » Thu, 2011-06-23 04:03
3
4,033 by nkemjika
Mon, 2014-04-21 06:47
Normal topic clustering in RosettaRemodel
by cheyuk » Wed, 2014-04-23 03:09
3
4,033 by rmoretti
Mon, 2014-05-12 08:45
Normal topic Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking
by Corvin » Wed, 2019-06-19 08:40
5
4,047 by rmoretti
Tue, 2019-07-09 10:13
Normal topic docking with constraints
by talavera » Tue, 2013-05-07 01:50
1
4,049 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaScripts - FastRelax loops
by jtmacd » Wed, 2015-11-18 09:32
2
4,052 by jtmacd
Fri, 2015-12-04 03:11
Normal topic Multistate design output
by tong » Wed, 2018-06-20 00:21
6
4,052 by tong
Sun, 2018-06-24 23:30
Normal topic "sparks failed" error when running "make_fragments.pl"?
by Danielsebas » Tue, 2019-09-03 03:43
6
4,056 by Jacob_Verburgt
Tue, 2020-03-10 14:39
Normal topic Not found some Flags
by jrcf » Sat, 2015-09-19 12:08
2
4,062 by jrcf
Mon, 2015-09-21 11:10
Normal topic flexpepdock flag "-packing:unboundrot"
by gw » Mon, 2011-07-11 12:23
2
4,074 by Ora Schueler-Furman
Mon, 2014-04-21 06:47
Normal topic Rosetta Holes
by zsun12 » Wed, 2015-09-30 11:40
1
4,090 by rmoretti
Mon, 2015-10-12 15:20
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
6
4,091 by chandana
Tue, 2022-08-09 20:27
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
4,092 by FJOM
Wed, 2023-05-03 07:21
Normal topic Problem with symmetric docking
by saxen » Fri, 2011-04-29 15:15
3
4,096 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to run simulations with non-canonical amino acids?
by Denise » Thu, 2017-06-08 07:50
4
4,099 by Denise
Thu, 2017-06-15 04:26
Normal topic Generate fragment file on my computer
by jrcf » Mon, 2015-09-21 15:41
2
4,101 by jrcf
Mon, 2015-10-05 21:32
Normal topic RosettaScripts LinkResidues
by Yero » Fri, 2019-05-17 05:26
5
4,127 by Yero
Thu, 2019-07-18 01:39
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43
3
4,148 by bjharris
Sun, 2020-08-23 14:03
Normal topic revert_design_to_native app comparison to FavorNativeResidue mover
by nwhoppe » Wed, 2016-06-29 14:35
3
4,149 by rmoretti
Tue, 2016-07-12 09:30
Normal topic Unsatisfied interface H-bond in Ligand docking
by Prasanth Kumar » Thu, 2013-07-18 12:04
1
4,158 by rmoretti
Mon, 2014-04-21 06:48
Normal topic RMSD calculation
by hamedkhakzad » Tue, 2016-09-13 04:56
2
4,161 by rmoretti
Wed, 2016-09-14 02:05
Normal topic Per residue scoring
by chelsell » Mon, 2015-08-17 14:43
3
4,164 by rmoretti
Wed, 2015-09-02 12:33
Normal topic ddg_monomer.mpi
by gw » Thu, 2011-10-27 16:45
3
4,169 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta 3.4 "Relax pdb with allatom constraints" does not work with structures containing multiple chains
by ahonegger » Tue, 2012-04-24 01:34
3
4,172 by ahonegger
Mon, 2014-04-21 06:47
Normal topic Constraints in RosettaCM
by kbuhr » Fri, 2015-07-31 06:55
3
4,180 by kbuhr
Mon, 2016-03-28 01:08
Normal topic null mutation with ddg_monomer
by fred » Fri, 2012-05-11 07:16
4
4,186 by fred
Mon, 2014-04-21 06:47
Normal topic partial ab initio modeling
by fred » Wed, 2011-08-17 14:14
3
4,188 by smlewis
Mon, 2014-04-21 06:47
Normal topic Changing scoring function for fixbb protocol
by mdyini » Sat, 2012-07-07 18:43
4
4,191 by mdyini
Mon, 2014-04-21 06:47
Normal topic rosetta3.4 fragment file problem
by David Hoover » Wed, 2012-05-16 14:42
4
4,201 by dgront
Mon, 2014-04-21 06:47
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