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Rosetta 3 - General

Topic / Topic starter Repliessort descending Views Last post
Normal topic de novo RNA loop
by c.ocasion » Sun, 2021-02-14 18:34
5
2,320 by everyday847
Mon, 2021-03-29 20:19
Normal topic Access sigma values for rotamers
by pachecoj » Thu, 2014-05-15 07:10
5
5,111 by rmoretti
Sat, 2014-05-17 14:10
Normal topic Chain specific flags
by helenah » Mon, 2020-10-19 03:31
5
2,589 by rmoretti
Fri, 2020-11-06 08:04
Normal topic rosetta_scripts_BOGUS coords warning message
by Karol » Tue, 2016-12-13 02:35
5
5,001 by Karol
Thu, 2016-12-15 01:35
Normal topic Problem with undetected lower and upper terminus variants for new polymer
by Martin Floor » Sat, 2022-06-11 06:51
5
1,455 by matteoferla
Fri, 2022-07-01 13:49
Normal topic Abinitio Calculations - typical parameters
by vamsi » Thu, 2010-11-11 07:06
5
5,545 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rotate MOVER
by gw » Wed, 2012-08-15 12:09
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4,999 by glemmon
Mon, 2014-04-21 06:47
Normal topic protein binding energy problem
by Lindsay » Thu, 2014-04-17 23:10
5
5,444 by jadolfbr
Mon, 2014-04-21 07:30
Normal topic Error when running "plot_LHOC.py"
by Sunyp_IM » Sun, 2017-08-13 05:54
5
3,881 by smlewis
Wed, 2017-08-16 08:30
Normal topic match_dspos1 and other matcher options
by petrikigor » Sat, 2012-10-20 09:22
5
5,209 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problems with disulphide bonds during KIC
by Loki01 » Tue, 2017-11-28 03:11
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3,930 by Loki01
Thu, 2017-12-14 06:20
Normal topic Modeling only part of the protein structure using ROSETTA
by qiongwu » Fri, 2009-05-29 09:08
5
4,564 by smlewis
Mon, 2014-04-21 06:47
Normal topic P-P docking with ambiguous constraints
by Anouk » Fri, 2013-11-08 11:38
5
6,280 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Rotamer Library Generation in Rosetta3
by jcminerlanl » Wed, 2016-11-30 07:34
5
5,295 by rmoretti
Tue, 2021-02-09 11:52
Normal topic BridgeChainsMover
by msardejani » Sun, 2016-08-07 17:32
5
4,597 by smlewis
Tue, 2016-08-30 13:47
Normal topic Relax command for docking purposes and cluster_vs_rmsd command
by Rkfoury » Wed, 2015-04-01 08:48
5
5,273 by rmoretti
Sat, 2015-04-25 10:05
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33
5
4,861 by rmoretti
Tue, 2014-11-18 10:01
Normal topic Typical relax options not applied in relax.mpi.linuxiccrelease??
by David Weis » Mon, 2017-02-27 11:35
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4,380 by rmoretti
Thu, 2017-08-03 09:01
Normal topic Rosetta-foldtree and docking
by tingting » Tue, 2022-03-15 22:49
5
1,511 by aastha.pal
Mon, 2022-06-27 09:55
Normal topic Evaluating energies on non-standard rotamer set
by pachecoj » Sat, 2014-07-26 16:27
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4,604 by pachecoj
Sat, 2014-08-09 06:33
Normal topic ClusterApp hogs way too much memory...
by IgaK » Tue, 2009-09-29 00:14
5
4,542 by w107kdk
Mon, 2014-04-21 06:47
Normal topic Efficient implementation of MPI with protein design programs
by zachdebruine » Thu, 2018-06-28 10:41
5
4,035 by smlewis
Tue, 2018-07-03 11:22
Normal topic Secondary Structure Relax
by ac.research » Sat, 2018-03-17 10:50
5
4,141 by smlewis
Wed, 2018-03-21 08:42
Normal topic Using 2 non-standard residues in one run
by einew » Tue, 2011-03-08 21:24
5
6,173 by einew
Mon, 2014-04-21 06:47
Normal topic Suppress printing to STDOUT for applications
by tylerborrman » Tue, 2015-11-24 11:37
5
5,103 by code_Monkey
Thu, 2021-03-18 08:03
Normal topic Resfile for fixed backbone design
by dyq » Wed, 2009-10-07 10:50
5
4,894 by attesor
Mon, 2014-04-21 06:47
Normal topic P(Res | phi,psi )
by jadolfbr » Thu, 2011-07-21 08:49
5
4,570 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic RosettaMatch
by jtmacd » Wed, 2012-01-11 06:50
5
9,507 by jtmacd
Mon, 2014-04-21 06:47
Normal topic industrial example of ROSETTA modeled protein
by banshee » Sat, 2016-04-23 23:40
5
4,801 by banshee
Tue, 2016-04-26 00:47
Normal topic How to extract specific pdb from silent files
by eunwook » Tue, 2013-05-14 05:29
5
14,750 by nawsad
Mon, 2014-04-21 06:47
Normal topic nr.fasta
by silvia » Wed, 2013-01-23 10:08
5
10,150 by dgront
Mon, 2014-04-21 06:47
Normal topic scoring models
by peony » Fri, 2013-12-06 02:45
5
5,471 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Minimization Issue: Coarse Graining to All atom modeling
by abolia » Tue, 2015-04-28 10:52
5
5,023 by rmoretti
Tue, 2015-05-05 14:31
Normal topic Cannot use SimpleMetrics
by Vedasheersh » Sun, 2018-06-10 23:38
5
3,511 by smlewis
Tue, 2018-06-12 10:54
Normal topic demos/public/ideal_proteins Segmentation fault
by coomteng@gmail.com » Wed, 2018-03-07 00:15
5
3,593 by rmoretti
Thu, 2018-03-08 07:46
Normal topic Error running snugdock
by SenyorDrew » Tue, 2017-03-14 10:00
5
4,281 by SenyorDrew
Wed, 2017-03-29 06:40
Normal topic Rosetta repacking output
by doranhen » Mon, 2012-12-03 03:44
5
5,591 by doranhen
Mon, 2014-04-21 06:47
Normal topic Make_fragments.pl database
by TiagoGomes » Tue, 2009-10-13 11:31
5
4,137 by matteoferla
Wed, 2021-09-29 01:58
Normal topic Robetta fragments and silent.out-file
by masterofpuppets » Wed, 2015-01-07 04:28
5
5,977 by masterofpuppets
Tue, 2015-02-10 03:15
Normal topic Docking double-stranded DNA to a protein
by xpzhang » Tue, 2012-01-31 12:35
5
8,478 by xpzhang
Mon, 2014-04-21 06:47
Normal topic Is cis-Glycine okay?
by matteoferla » Tue, 2019-11-19 07:26
5
3,078 by matteoferla
Wed, 2019-11-20 02:32
Normal topic Unrecognized residue Glc
by cgautier » Tue, 2015-03-31 02:20
5
5,907 by rmoretti
Thu, 2015-04-16 10:09
Normal topic Encouraging better packing in enzyme_design
by linucks » Thu, 2018-03-01 07:05
5
5,169 by linucks
Wed, 2018-04-25 08:50
Normal topic Produces a set of rotamers from a given residue
by a-eatemadi@razi... » Tue, 2017-08-15 08:05
5
4,840 by a-eatemadi@razi...
Fri, 2017-09-15 07:45
Normal topic defining interface in interface analyzer
by aa20 » Fri, 2013-09-27 11:08
5
6,501 by smlewis
Mon, 2014-04-21 06:48
Normal topic segmentation fault when using design_hpatch scoring function
by rbjacob » Mon, 2018-04-09 11:05
5
3,473 by smlewis
Wed, 2018-04-11 11:45
Normal topic dun10
by jadolfbr » Thu, 2012-01-19 12:16
5
4,800 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Scoring Electrostatics
by aroop » Tue, 2012-08-07 11:41
5
5,185 by aroop
Mon, 2014-04-21 06:47
Normal topic modeling residues with covalent ligand attachments
by sid » Fri, 2011-04-15 09:16
5
7,359 by rmoretti
Fri, 2015-07-03 14:02
Normal topic Rosetta Antibody Prepack - Problem HL_A vs. LH_A
by cannond » Fri, 2017-03-03 02:41
5
4,873 by cannond
Wed, 2017-03-08 03:00
Normal topic calculated ddG_bind converges to zero
by fukamitka » Mon, 2013-06-24 20:32
6
5,603 by fukamitka
Mon, 2014-04-21 06:48
Normal topic AbinitioRelax under different directories without -constant_seed -jran flag
by xpzhang » Wed, 2010-09-15 14:56
6
7,181 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problem with clustering 1000 centroid pdbs
by doranhen » Sat, 2012-04-28 10:34
6
6,265 by doranhen
Mon, 2014-04-21 06:47
Normal topic Linker problems when building mini
by assaff » Mon, 2009-10-12 01:07
6
5,005 by smlewis
Mon, 2014-04-21 06:47
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43
6
5,141 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Memory leak when PDB preparation
by Jacky010 » Mon, 2019-05-06 01:28
6
3,739 by Jacky010
Tue, 2019-05-14 01:24
Normal topic SASA packing score in Rosetta 3.1
by enoee » Wed, 2010-07-28 01:45
6
6,386 by smlewis
Mon, 2014-04-21 06:47
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30
6
13,192 by rmoretti
Mon, 2014-04-21 06:47
Normal topic This element is not expected.
by ac.research » Fri, 2017-10-13 03:47
6
6,633 by vmulligan
Thu, 2020-07-16 23:31
Normal topic Fe3p Heme Iron Unrecognized Despite Loading Hem Params
by vsjasion » Fri, 2011-09-02 10:37
6
7,194 by tigerous
Mon, 2014-04-21 06:47
Normal topic Relax structure using Membrane Environment Scoring Function
by anna.duncan » Thu, 2010-02-04 08:01
6
7,536 by jruhym
Mon, 2014-04-21 06:47
Normal topic Cannot run binaries after successful compilation
by ac.research » Mon, 2017-08-14 02:56
6
6,608 by ac.research
Fri, 2017-08-18 00:57
Normal topic Can i start again the job ?
by byin » Thu, 2011-09-15 01:19
6
5,056 by byin
Mon, 2014-04-21 06:47
Normal topic NR Database Download in install_dependencies.pl (for make_fragments.pl) Broken
by Jacob_Verburgt » Tue, 2020-03-10 08:58
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4,713 by Jacob_Verburgt
Wed, 2020-03-11 05:18
Normal topic ERROR: compiling rosetta3.1 with MPI
by biofisikx » Thu, 2010-08-05 16:00
6
6,107 by smlewis
Mon, 2014-04-21 06:47
Normal topic dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.
by jyotisutar9 » Thu, 2016-12-01 00:39
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5,428 by jyotisutar9
Wed, 2016-12-14 09:39
Normal topic Using Patches in Rosetta
by JS » Wed, 2010-03-10 13:32
6
7,694 by JS
Mon, 2014-04-21 06:47
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
861 by rmoretti
Mon, 2023-02-20 16:07
Normal topic distances definition in course-grained (centroid mode) steps
by allan.ferrari » Tue, 2017-01-03 05:15
6
4,864 by allan.ferrari
Tue, 2017-01-03 11:15
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
6
3,539 by jadolfbr
Thu, 2020-09-24 10:04
Normal topic What's a good application to thread a sequence over a peptide (of a peptide-protein complex) and minimize?
by brspurri » Tue, 2013-02-12 08:19
6
6,744 by smlewis
Mon, 2014-04-21 06:47
Normal topic is it possible to ab initio only a part of a protein?
by albumns » Sun, 2011-02-13 08:10
6
4,552 by albumns
Mon, 2014-04-21 06:47
Normal topic The design of a helical peptide
by Jacob-kong » Tue, 2012-06-26 06:26
6
7,770 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic abinitiorelax: No funnel
by cno » Tue, 2010-07-27 06:14
6
5,160 by biofisikx
Mon, 2014-04-21 06:47
Normal topic pdb files in Rosetta format
by zhisheng » Mon, 2011-10-31 08:52
6
6,823 by smlewis
Mon, 2014-04-21 06:47
Normal topic Don't want to output the design structure
by Lindsay » Wed, 2012-05-02 08:02
6
5,314 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Atomic refinement with fixed ligand
by ahmadkhalifa » Tue, 2018-07-24 10:41
6
4,231 by rmoretti
Mon, 2018-08-20 11:45
Normal topic No score.sc generated after running flexpepdock.
by monos_morpheus » Sun, 2011-04-10 04:06
6
5,769 by robren
Mon, 2014-04-21 06:47
Normal topic Rosetta CM incorrect threading
by ahmadkhalifa » Mon, 2018-08-06 11:09
6
4,592 by rmoretti
Fri, 2018-08-24 11:59
Normal topic How to run Rosetta3 in parallel
by lennylv » Mon, 2009-03-30 04:21
6
9,185 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Rosetta CM - Ignore Sporadic Errors
by Swillard » Wed, 2018-06-13 05:47
6
4,100 by rmoretti
Mon, 2018-11-12 14:29
Normal topic Problem With Rosetta3.3 Comparative/Loop Modeling And Constraints
by jurkm » Mon, 2011-09-12 01:01
6
5,833 by jurkm
Mon, 2014-04-21 06:47
Normal topic '-norepack_disulf' flag NOT work in Ligand-protein docking ?
by darlintai » Tue, 2011-01-11 22:21
6
5,774 by smlewis
Mon, 2014-04-21 06:47
Normal topic Public subversion / Enzyme design public app
by weallen » Tue, 2009-08-11 20:50
6
4,994 by weallen
Mon, 2014-04-21 06:47
Normal topic two questions about "Prepare structures for use in Rosetta"
by Anonymous » Wed, 2012-06-06 08:13
6
5,625 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Energy Calculation in Rosetta3.4
by sdg_lab » Thu, 2012-04-12 04:49
6
10,830 by rmoretti
Mon, 2014-04-21 06:47
Normal topic mitochondria protein modeling
by rlwoltz » Fri, 2012-10-26 14:32
6
6,432 by smlewis
Mon, 2014-04-21 06:47
Normal topic what rotamer lib is used in rosetta3.5?
by Lindsay » Thu, 2014-02-06 16:11
6
5,846 by rmoretti
Fri, 2014-03-28 09:03
Normal topic Add a ligand with only one atom (i.e. Zn) to the RosettaCM
by lanselibai » Tue, 2021-06-22 10:28
6
2,192 by rmoretti
Thu, 2021-06-24 12:23
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
6,061 by smlewis
Mon, 2014-04-21 06:47
Normal topic optH flag makes hydrogen bond energy scores worse...
by tsjain » Fri, 2012-07-13 14:04
6
6,298 by smlewis
Mon, 2014-04-21 06:47
Normal topic selecting pivot_residue in Backrub for ensemble generation
by rohi » Fri, 2020-08-07 15:41
6
3,470 by matteoferla
Tue, 2020-08-11 10:00
Normal topic Native gives higher (positive) than lowest energy and clustered decoys
by tiagogomes89 » Thu, 2011-06-02 07:19
6
5,196 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaDock - protonation states
by LWilliamson » Tue, 2023-08-15 08:15
6
322 by nannemdp
Thu, 2023-08-24 08:21
Normal topic modeling loops between domains
by dhorita » Thu, 2009-03-05 14:48
6
5,280 by jarod
Mon, 2014-04-21 06:47
Normal topic ERROR: beta_nov16(.wts) requested, but -corrections::beta_nov16 not set to true. This leads to a garbage scorefunction.
by sia » Mon, 2023-05-08 06:36
6
532 by rmoretti
Tue, 2023-05-16 07:10
Normal topic membrane ab initio error after montecarlo
by adva » Mon, 2012-12-24 01:43
6
5,707 by tevang
Mon, 2014-04-21 06:47
Normal topic Comparative Modeling databases?
by nitroamos » Wed, 2011-11-23 14:54
6
5,886 by rmoretti
Thu, 2016-04-28 16:15
Normal topic RosettaHoles
by ge0rgekh0ury » Mon, 2012-01-09 09:01
6
5,768 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Fixed bb design with hydrogen bond constraint
by bharat_46010 » Mon, 2012-04-30 22:56
6
5,624 by smlewis
Mon, 2014-04-21 06:47
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