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Rosetta 3 - Applications

Topic / Topic starter Replies Viewssort descending Last post
Normal topic Difference between relax and mimimize_with_cst
by basvandenberg » Thu, 2012-02-09 00:16
1
2,174 by rmoretti
Mon, 2014-04-21 06:47
Normal topic residues_patch_selectors CENTROID_HA
by Pernille » Fri, 2014-10-03 03:53
2
2,180 by Pernille
Wed, 2014-10-08 10:41
Normal topic refining crystal structure using phenix without CIF file
by banshee » Fri, 2016-09-09 01:14
2
2,193 by banshee
Mon, 2016-09-12 23:41
Normal topic RosettaCM input file for running on Stampede
by smathersc » Wed, 2017-01-18 16:12
3
2,195 by rmoretti
Thu, 2017-02-02 09:02
Normal topic Binding energy contribution broken down by residue
by brspurri » Tue, 2013-07-23 12:47
1
2,196 by rmoretti
Mon, 2014-04-21 06:48
Normal topic profit program in antibody design
by tzhou » Tue, 2013-10-15 23:29
1
2,198 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'
by smiruthi » Mon, 2011-12-12 14:27
1
2,204 by rmoretti
Mon, 2014-04-21 06:47
Normal topic docking with constraints and flexible bb
by mintseris » Mon, 2015-06-22 09:07
2
2,206 by mintseris
Wed, 2015-06-24 22:04
Normal topic Flexible peptide docking with flexible receptor backbone
by tevang » Fri, 2012-09-14 11:18
1
2,206 by smlewis
Mon, 2014-04-21 06:47
Normal topic Options for Enzdes RosettaScripts
by joeg » Wed, 2014-03-12 09:28
1
2,212 by rmoretti
Thu, 2014-03-13 08:04
Normal topic Unexpected Error with RosettaCM -
by terry » Fri, 2019-02-22 14:26
1
2,222 by rmoretti
Fri, 2019-03-29 12:25
Normal topic ERROR: Rosetta does not recognize the property: SIDECHAIN_THIOL, when running minimize_with_cst.linuxgccrelease
by cossio » Thu, 2015-09-03 08:46
1
2,224 by rmoretti
Fri, 2015-09-04 10:25
Normal topic How to preserve ACE/NME termini?
by nitroamos » Tue, 2018-05-22 13:07
3
2,225 by rmoretti
Thu, 2018-06-28 12:44
Normal topic Pre-packing a model for SWA loop building
by franfdez » Sun, 2014-07-27 02:16
2
2,229 by franfdez
Mon, 2014-07-28 01:04
Normal topic ab initio
by malkeet.singh » Thu, 2018-05-10 05:34
3
2,233 by malkeet.singh
Mon, 2018-05-21 04:26
Normal topic Adding water interactions when docking a ligand with Rosetta 3.7.
by brspurri » Thu, 2017-06-01 09:37
2
2,234 by brspurri
Thu, 2017-06-01 10:58
Normal topic very good I_sc values (if not too good)
by attesor » Tue, 2015-11-03 03:30
2
2,239 by attesor
Tue, 2015-11-17 07:36
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,240 by smlewis
Mon, 2014-04-21 06:47
Normal topic Use NMR ensemble in protein-protein docking?
by cossio » Sun, 2015-09-13 07:57
2
2,243 by cossio
Tue, 2015-09-15 12:48
Normal topic How to calculate dG?
by yperez » Mon, 2012-10-22 07:28
1
2,245 by smlewis
Mon, 2014-04-21 06:47
Normal topic Snugdock+ensembledock usage
by Anouk » Mon, 2014-09-22 08:09
1
2,246 by jadolfbr
Mon, 2014-10-20 13:42
Normal topic Destination of score.fsc file
by anirbanzz » Wed, 2011-04-20 23:30
1
2,255 by smlewis
Mon, 2014-04-21 06:47
Normal topic No interface for protein - Interface Analyzer
by aloshbau » Tue, 2013-05-21 21:00
1
2,255 by jarod
Mon, 2014-04-21 06:47
Normal topic Extract PDB structures from database
by cossio » Mon, 2018-01-29 09:30
3
2,259 by rmoretti
Fri, 2018-11-23 11:23
Normal topic cluster error
by sudhar » Fri, 2011-06-17 05:58
1
2,262 by rmoretti
Mon, 2014-04-21 06:47
Normal topic membrane score weights
by ytao » Sat, 2012-09-08 06:56
2
2,265 by ytao
Mon, 2014-04-21 06:47
Normal topic ROSETTALIGAND: How to prepare data to plot ROC curves using rosettaligand docking result???
by Ryhon Wang » Mon, 2016-01-04 22:36
1
2,279 by rmoretti
Tue, 2016-01-05 08:35
Normal topic Docking on mpi.
by Pernille » Mon, 2014-07-28 08:40
1
2,284 by rmoretti
Mon, 2014-08-04 14:51
Normal topic Floppy tail: sidechain mutation during calculation
by syoifczeri » Mon, 2015-03-09 19:01
2
2,285 by syoifczeri
Tue, 2015-03-10 23:08
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43
3
2,289 by bjharris
Sun, 2020-08-23 14:03
Normal topic RosettaSurface in 3.4?
by skovacs » Tue, 2012-07-10 16:02
2
2,293 by mpacella
Mon, 2014-04-21 06:47
Normal topic Reproduce Robetta's ddg values of interface alanine scan using Rosetta?
by cossio » Mon, 2015-01-19 07:14
0
2,309 by cossio
Mon, 2015-01-19 07:14
Normal topic Connecting linkers
by Prasanth Kumar » Tue, 2014-05-06 00:53
1
2,314 by smlewis
Mon, 2014-05-12 08:32
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37
3
2,319 by rmoretti
Tue, 2017-10-10 09:58
Normal topic homology membrane modeling demo in rosetta 3.5
by rlwoltz » Mon, 2013-09-09 10:26
1
2,333 by smlewis
Mon, 2014-04-21 06:48
Normal topic Fold and Dock - chains not in contact
by arthuc01 » Wed, 2012-06-13 01:45
2
2,344 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26
1
2,361 by everyday847
Wed, 2017-05-17 20:03
Normal topic Fragment Files
by nkemjika » Fri, 2011-07-22 15:11
1
2,367 by dgront
Mon, 2014-04-21 06:47
Normal topic ProteinLigandInterfaceUpweighter for protein-protein interactions?
by ahonegger » Mon, 2014-06-02 06:53
2
2,371 by ahonegger
Fri, 2014-06-06 09:31
Normal topic Problems incorporating nucleotides (GTP/GDP) into the modeling process for RosettaCM
by ajkal » Fri, 2017-04-14 08:44
3
2,374 by rmoretti
Thu, 2017-04-20 13:59
Normal topic Membrane homology modeling loop building gives very strange outputs
by chelsell » Tue, 2014-09-30 14:46
2
2,374 by chelsell
Wed, 2014-10-08 12:25
Normal topic Relax is resulting in a Segmentation Fault
by brspurri » Thu, 2017-08-24 18:46
3
2,376 by brspurri
Sat, 2017-08-26 07:08
Normal topic where to look for positive sign for solution in mr-rosetta3.4?
by lchen » Tue, 2012-07-10 09:38
2
2,383 by lchen
Mon, 2014-04-21 06:47
Normal topic Fragments for long sequence
by exchhattu » Tue, 2011-10-04 01:51
2
2,391 by exchhattu
Mon, 2014-04-21 06:47
Normal topic SymDock with constraints
by felipet » Thu, 2015-05-14 09:01
1
2,391 by rmoretti
Mon, 2015-05-25 11:49
Normal topic How to use Rosetta to DISCARD a protein-protein docking interface?
by cossio » Tue, 2015-05-26 06:24
2
2,391 by rmoretti
Sat, 2015-07-11 13:38
Normal topic conformational sampling of multi domain protein
by dhirajks » Tue, 2017-07-04 11:20
4
2,394 by jrporter
Wed, 2017-07-05 06:30
Normal topic Flexpep docking freezing issue at "press enter to continue"
by rlwoltz » Tue, 2013-01-22 13:31
2
2,403 by rlwoltz
Mon, 2014-04-21 06:47
Normal topic How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?
by lanselibai » Sat, 2015-01-17 11:19
1
2,406 by lanselibai
Wed, 2015-01-21 02:40
Normal topic RosettaScripts LinkResidues
by Yero » Fri, 2019-05-17 05:26
5
2,409 by Yero
Thu, 2019-07-18 01:39
Normal topic Threading a sequence onto a template with ligands/metal ions included
by ajkal » Wed, 2017-04-19 11:53
3
2,410 by ahmadkhalifa
Sun, 2019-03-31 23:27
Normal topic Multistate design output
by tong » Wed, 2018-06-20 00:21
6
2,410 by tong
Sun, 2018-06-24 23:30
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,412 by jharamesh
Mon, 2014-11-03 12:50
Normal topic clustering
by ays » Tue, 2014-09-30 08:26
2
2,415 by rmoretti
Mon, 2014-10-06 16:00
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
2,416 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic mr_protocols with symmetry and ligand
by jhm13c » Mon, 2017-02-27 11:59
4
2,431 by jhm13c
Thu, 2017-03-02 12:01
Normal topic How to add constrains to FlexPepDocking?
by MajorID » Thu, 2011-06-02 11:00
2
2,432 by MajorID
Mon, 2014-04-21 06:47
Normal topic Error with -patch_selectors
by subha » Tue, 2017-06-06 14:40
4
2,432 by subha
Fri, 2017-06-09 15:42
Normal topic Full Protocol
by shekhar » Fri, 2013-10-04 01:07
1
2,443 by rmoretti
Mon, 2014-04-21 06:48
Normal topic dihedral_between_bonded_children: atoms are not both my children!
by pdbb » Fri, 2013-04-05 06:40
3
2,444 by smlewis
Mon, 2014-04-21 06:47
Normal topic Segmentation fault when running Abinito Relax
by Hongtham » Mon, 2014-12-15 07:16
1
2,444 by rmoretti
Fri, 2015-01-02 11:45
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
2,445 by Wizard
Sun, 2015-04-26 22:36
Normal topic side chain repacking error
by malkeet.singh » Thu, 2017-12-07 04:49
4
2,446 by smlewis
Wed, 2017-12-13 09:54
Normal topic Symmetry definition for apolar helix
by vanrooyenjason » Tue, 2016-01-05 05:20
1
2,447 by rmoretti
Fri, 2016-04-29 09:21
Normal topic No Space
by jrcf » Mon, 2016-01-11 16:18
3
2,457 by jrcf
Fri, 2016-02-12 16:42
Normal topic FlexPepDock and total score problem
by tkellici » Fri, 2014-01-17 06:07
2
2,459 by Ora Schueler-Furman
Mon, 2014-04-21 06:48
Normal topic how to reconstruct the whole complex after symmetric docking
by Anonymous » Tue, 2012-07-03 02:44
2
2,468 by felipet
Wed, 2014-07-02 07:26
Normal topic loopmodel issue
by chiendarret » Fri, 2012-01-27 00:51
1
2,474 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
2,476 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic De novo model-building guided by exprimental density data
by dee2711453 » Thu, 2016-03-10 17:28
3
2,480 by dee2711453
Fri, 2016-03-11 21:32
Normal topic  The error of InterfaceAnalyzer
by asbelx » Thu, 2017-12-21 19:04
3
2,494 by smlewis
Sat, 2017-12-23 15:56
Normal topic ab initio modelling - what to do next?
by krlitros87 » Thu, 2014-10-16 13:05
2
2,498 by krlitros87
Wed, 2014-10-22 09:31
Normal topic PIKAA in resfile does not mutate Cys in disulfide bond to specified residue
by attesor » Fri, 2014-03-14 07:53
2
2,499 by attesor
Mon, 2014-06-16 07:34
Normal topic prepack_example.sh error message
by sacch » Sun, 2011-10-23 23:22
2
2,505 by sacch
Mon, 2014-04-21 06:47
Normal topic RMS determination using Rosetta 3.3
by adraney » Thu, 2011-12-08 12:44
2
2,515 by mark.wilson
Mon, 2014-04-21 06:47
Normal topic high-res docking
by tfliu » Mon, 2013-07-15 02:49
2
2,520 by tfliu
Mon, 2014-04-21 06:48
Normal topic Modeling flexible linkers with Floppytail
by pdbb » Sun, 2013-05-12 15:55
2
2,520 by smlewis
Mon, 2014-04-21 06:47
Normal topic problem when exact pdb from silent file
by wenchangyu2008 » Mon, 2011-04-18 00:42
1
2,522 by wenchangyu2008
Mon, 2014-04-21 06:47
Normal topic Docking Prepack protocol working or not ?
by MJG » Mon, 2017-04-03 08:02
4
2,524 by MJG
Tue, 2017-04-04 23:59
Normal topic scoring input pdbs as the same as docking score
by hamedkhakzad » Fri, 2016-07-01 07:15
3
2,526 by rmoretti
Tue, 2016-07-12 09:05
Normal topic Local docking: "manually place the two proteins facing each other" ?
by mdeklotz » Fri, 2018-07-20 10:24
5
2,533 by dfcoelho
Tue, 2018-10-16 09:05
Normal topic kinematic loop modeling multiple input: possible?
by a_s_a » Thu, 2011-05-12 09:33
2
2,537 by a_s_a
Mon, 2014-04-21 06:47
Normal topic std::bad_alloc error after changing .xml script?
by chrisHKL » Wed, 2020-03-04 11:44
10
2,539 by jadolfbr
Thu, 2020-03-05 07:02
Normal topic do mpi apps share memory?
by fred » Thu, 2014-01-23 11:49
2
2,542 by fred
Mon, 2014-04-21 06:48
Normal topic select_best_unique_ligand_poses output
by ast » Thu, 2013-07-11 02:33
2
2,543 by ast
Mon, 2014-04-21 06:48
Normal topic Fnat and Irms are nan in score.sc from docking_protocol?
by cossio » Sun, 2015-09-13 07:34
2
2,554 by rmoretti
Thu, 2015-09-17 12:47
Normal topic Total score problems with high-res ddg_monomer
by jklesmith » Tue, 2015-03-10 15:54
2
2,563 by jennifer
Fri, 2015-03-27 05:56
Normal topic ambiguous constraints
by shrutikhare » Mon, 2014-05-12 04:42
1
2,577 by rmoretti
Mon, 2014-05-12 08:25
Normal topic Abinito for Multimers
by Prasanth Kumar » Wed, 2014-01-22 17:45
2
2,578 by Prasanth Kumar
Mon, 2014-04-21 06:48
Normal topic Symmetric docking with multiple chains as asymmetric unit
by sarah29 » Tue, 2013-11-05 20:24
1
2,581 by rmoretti
Mon, 2014-04-21 06:48
Normal topic placing a constraint during structure prediction
by cbala » Thu, 2011-04-07 08:54
1
2,591 by ic3reyes
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
2,592 by brspurri
Fri, 2017-03-24 11:35
Normal topic rosetta app
by MA » Wed, 2017-07-05 06:52
5
2,596 by smlewis
Tue, 2017-07-11 07:53
Normal topic Use "loopmodel.linuxgccrelease" CCD to build missing residue positions
by lanselibai » Sun, 2014-10-12 09:00
2
2,597 by lanselibai
Mon, 2014-10-13 10:10
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Tue, 2011-02-15 17:23
2
2,600 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
2,618 by ahonegger
Mon, 2014-05-12 09:08
Normal topic error with fragment_picker.linuxgccrelease
by jiongzhang » Tue, 2012-04-17 09:07
3
2,624 by smlewis
Mon, 2014-04-21 06:47
Normal topic DDG monomer and backrub motions
by yperez » Thu, 2012-06-21 08:10
2
2,626 by yperez
Mon, 2014-04-21 06:47
Normal topic running in MPI mode and multiple scores per output PDB file?
by dantimatter » Wed, 2019-10-30 09:42
7
2,636 by dantimatter
Wed, 2019-11-06 09:51
Normal topic Does relax.linuxgccrelease fully relax the structure compared to ddg_monomer.linuxgccrelease?
by lanselibai » Thu, 2015-01-08 03:23
3
2,650 by lanselibai
Tue, 2015-01-13 14:25
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