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Rosetta 3 - General

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Normal topic How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?
by johnnytam100 » Wed, 2019-05-08 02:30
2
2,947 by johnnytam100
Wed, 2019-05-15 18:45
Normal topic The -symmetry:perturb_rigid_body_dofs flag
by doranhen » Sat, 2012-04-28 13:01
2
2,905 by doranhen
Mon, 2014-04-21 06:47
Normal topic Write PDB with multiple side-chain configurations
by pachecoj » Tue, 2014-09-30 21:42
2
3,106 by pachecoj
Thu, 2014-10-09 18:15
Normal topic Expanding the silent file
by jharamesh » Fri, 2018-01-12 09:15
2
2,173 by rmoretti
Mon, 2018-01-15 14:35
Normal topic Undocumented changes in BackrubDD
by abhi_pe_acharya » Mon, 2018-07-16 00:24
2
2,143 by abhi_pe_acharya
Sun, 2018-08-05 22:03
Normal topic protein surface design
by tatsiana.bylund » Sun, 2019-09-15 03:44
2
2,066 by dfcoelho
Tue, 2019-11-19 10:16
Normal topic fixbb design use
by Lindsay » Fri, 2012-03-23 09:05
2
2,941 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Radius of Gyration
by ctaylor » Mon, 2009-09-21 12:45
2
4,412 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18
2
5,214 by pepfolder
Mon, 2014-04-21 06:47
Normal topic Loop Modelling: ERROR: switch_to_residue_type_set fails
by smiruthi » Wed, 2012-07-18 14:48
2
3,646 by smlewis
Mon, 2014-04-21 06:47
Normal topic symmetric docking application rosetta3.2: the docking_local_refine flag
by doranhen » Sun, 2012-05-06 02:20
2
3,247 by doranhen
Mon, 2014-04-21 06:47
Normal topic sign of ddG of mutation
by Lindsay » Wed, 2013-11-27 00:25
2
4,809 by Lindsay
Mon, 2014-04-21 06:48
Normal topic Calculating binding affinity
by phanvy » Wed, 2014-10-15 23:35
2
4,747 by phanvy
Thu, 2014-10-16 18:54
Normal topic Repeating sequence in Rosetta de novo protein folding
by orionshih » Wed, 2018-02-07 20:52
2
2,201 by sheehajh
Thu, 2018-02-08 21:18
Normal topic perturb_temp flag
by Loki01 » Tue, 2018-11-27 05:06
2
2,085 by rmoretti
Wed, 2019-04-03 09:58
Normal topic Ligand being read as part of protein structure
by MarkusAurelius » Thu, 2021-04-01 11:00
2
1,788 by MarkusAurelius
Fri, 2021-04-02 11:44
Normal topic genkic mover produced an unwanted HN - CA bond
by cttm4a1 » Mon, 2022-06-20 14:25
2
1,059 by cttm4a1
Mon, 2022-06-20 16:58
Normal topic Bug in Loop Modeling
by dseelig » Thu, 2010-09-23 05:55
2
2,895 by smlewis
Mon, 2014-04-21 06:47
Normal topic Checkpoints in Rosetta
by exchhattu » Mon, 2009-10-19 17:47
2
3,156 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Rosetta forcefield terms and interpretation
by zigeuner » Sat, 2013-05-25 16:59
2
5,063 by rmoretti
Mon, 2014-04-21 06:47
Normal topic dG/dsasa , What is the exact meaning?
by Apiwat » Sun, 2014-04-13 00:38
2
4,531 by Apiwat
Thu, 2014-04-17 09:56
Normal topic Rosetta CM round_thread.pdb doesn't exist and can't find pose (id = round)
by ahmadkhalifa » Wed, 2018-05-23 09:51
2
3,591 by rmoretti
Thu, 2018-06-28 14:09
Normal topic 4mer 6mer fragment database
by bjharris » Wed, 2020-09-09 15:12
2
1,873 by bjharris
Wed, 2020-09-09 20:04
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
1,549 by patcD
Wed, 2021-09-01 06:54
Normal topic pose.energies().total_enegies().show_nonzero() changes after packer is applied
by Liviu Copoiu » Mon, 2022-11-07 16:51
2
1,024 by Liviu Copoiu
Tue, 2022-11-08 10:43
Normal topic Structure Prediction: Max Sequence Length?
by jcsaborio » Tue, 2009-07-14 12:10
2
4,125 by jcsaborio
Mon, 2014-04-21 06:47
Normal topic Run PackRotamersMover on specified rotamer set
by pachecoj » Mon, 2014-11-10 06:51
2
2,952 by pachecoj
Tue, 2014-11-11 19:30
Normal topic Method for WebServer Fragment Generation
by Jacob_Verburgt » Tue, 2020-06-02 07:29
2
2,090 by Jacob_Verburgt
Tue, 2020-06-02 10:26
Normal topic Output and Input Tutorial
by jgustat » Fri, 2022-07-01 13:07
2
1,092 by jgustat
Fri, 2022-07-01 13:26
Normal topic ddG backbone movement
by dave » Wed, 2012-10-03 03:23
2
3,148 by dave
Mon, 2014-04-21 06:47
Normal topic Do Rosetta support hydroxide(OH-) and oxide(O2-) params?
by dasdevashishdas » Thu, 2018-08-16 21:15
2
2,358 by dasdevashishdas
Thu, 2018-08-23 18:02
Normal topic Running time of Rosetta/FlexPepDock
by gerdos » Thu, 2015-10-15 02:14
2
2,808 by gerdos
Fri, 2015-10-16 03:01
Normal topic Job Distribution Error
by ac.research » Mon, 2020-02-10 08:22
2
2,121 by ac.research
Fri, 2020-02-14 23:33
Normal topic RuntimeError: CUDA out of memory.
by ravi.thakkar » Tue, 2023-03-07 00:27
2
961 by rmoretti
Tue, 2023-03-07 08:18
Normal topic Loop modelling,
by berk » Sat, 2013-06-08 08:29
2
2,920 by berk
Mon, 2014-04-21 06:48
Normal topic How to generate symmdef file for translational symmetry only?
by pitmand » Thu, 2015-05-14 11:34
2
3,201 by pitmand
Tue, 2015-05-26 12:20
Normal topic ligand dock residue selection
by Silice » Wed, 2009-08-12 08:57
2
2,979 by frichter
Mon, 2014-04-21 06:47
Normal topic Clustering Rosetta output PDB files
by ritacc18 » Sat, 2014-01-11 20:13
2
5,787 by jwillis
Sat, 2015-06-27 21:11
Normal topic What is "residue packing", "repacking", and so on?
by cossio » Wed, 2014-12-03 08:49
2
3,857 by cossio
Wed, 2014-12-03 14:51
Normal topic scoring with omega energy term
by SergeyP » Thu, 2017-03-09 12:03
2
2,774 by SergeyP
Fri, 2017-03-10 11:16
Normal topic FARFAR2 Error With Secondary Structure File
by bdh81 » Thu, 2023-11-02 09:01
2
578 by bdh81
Sun, 2023-11-05 16:04
Normal topic Rosetta numbering with missing occupancies
by ShaneOConnor » Fri, 2011-10-07 16:18
2
3,675 by ShaneOConnor
Mon, 2014-04-21 06:47
Normal topic RASREC - finding lowest energy structure
by Lati » Fri, 2015-11-20 03:08
2
2,966 by Lati
Tue, 2016-01-12 13:28
Normal topic DockingProtocol mover ensemble error
by dfcoelho » Tue, 2018-10-16 08:32
2
2,698 by brspurri
Thu, 2020-08-20 13:22
Normal topic Rigid Body & Flexible Minimization
by Hanieh » Thu, 2014-02-06 12:37
2
4,058 by Hanieh
Fri, 2014-02-28 12:43
Normal topic Error reading new residue .param file
by mgrom92 » Tue, 2016-03-22 12:54
2
4,486 by mgrom92
Wed, 2016-03-23 16:45
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32
2
1,111 by Ken
Wed, 2022-08-17 08:04
Normal topic Using mode=profile
by Biokhar » Fri, 2012-07-06 00:29
2
3,889 by scombs
Mon, 2014-04-21 06:47
Normal topic How to prevent rotamers from being pruned from the interaction graph?
by msun » Wed, 2013-04-17 14:19
2
2,955 by smlewis
Mon, 2014-04-21 06:47
Normal topic Adding centroid .params files for non-canonical residues based on all-atom .params files
by jcminerlanl » Thu, 2017-04-27 09:28
2
2,707 by vmulligan
Thu, 2017-04-27 16:41
Normal topic The concept of unsatisfied hydrogen bond
by asbelx » Wed, 2018-04-25 01:32
2
3,353 by asbelx
Thu, 2018-04-26 00:23
Normal topic Controlling Input in the Tutorial
by Smbat » Wed, 2020-07-29 22:41
2
1,766 by Smbat
Thu, 2020-07-30 03:07
Normal topic Differences between energy values reported in the tutorials and the ones obtained by running the code, what is normal?
by ericlang » Mon, 2021-07-05 05:43
2
1,354 by ericlang
Mon, 2021-07-05 06:59
Normal topic Specifying sidechain NOE restraints in Relax!
by kalabharath » Mon, 2012-12-10 16:44
2
3,136 by kalabharath
Mon, 2014-04-21 06:47
Normal topic Using NCAAs in protocols with native heme proteins
by htorres » Wed, 2018-01-24 08:32
2
2,837 by htorres
Mon, 2018-02-05 06:53
Normal topic de novo protein prediction
by pci112 » Tue, 2021-03-23 10:13
2
1,619 by pci112
Thu, 2021-03-25 01:44
Normal topic activation of filters in rosetta3.0 or later
by exchhattu » Thu, 2009-12-03 17:52
2
2,871 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Does Rosetta have a separate refinement function?
by ylwang » Tue, 2019-09-24 19:08
2
2,076 by ylwang
Tue, 2019-10-08 18:34
Normal topic mode=release compile on a mac-pro , seg faults and bus errors
by dnasmith » Thu, 2010-09-09 16:56
2
2,607 by dnasmith
Mon, 2014-04-21 06:47
Normal topic all-atom refinement with Relax application
by zwenthor » Mon, 2010-02-15 22:45
2
2,982 by zwenthor
Mon, 2014-04-21 06:47
Normal topic -RBSegmentRelax:cst_wt not present in ca_to_allatom.linuxgccrelease application?
by Karol » Thu, 2016-05-12 06:30
2
2,715 by Karol
Thu, 2016-05-12 07:58
Normal topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:18
2
2,259 by jalan
Sun, 2020-04-12 08:01
Normal topic Residue variant types and fragments
by jadolfbr » Mon, 2013-01-21 09:01
2
3,342 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic No RMS and IRMS values in protein/nucleic acid docking
by rbeier1 » Wed, 2016-01-13 12:41
2
3,422 by smlewis
Thu, 2016-01-14 08:19
Normal topic Error in flex ddG tutorial
by wentlewi » Sat, 2020-05-16 08:06
2
1,983 by Alvin Yang
Wed, 2023-10-04 03:34
Normal topic De novo backbone trace from fragments
by Victor Tobiasson » Tue, 2020-12-22 06:34
2
2,050 by Victor Tobiasson
Tue, 2020-12-22 09:18
Normal topic relax with restraints
by jtmacd » Mon, 2010-11-08 09:11
2
2,934 by jtmacd
Mon, 2014-04-21 06:47
Normal topic make fragments for a loop
by jarod » Mon, 2010-03-15 07:31
2
2,894 by jarod
Mon, 2014-04-21 06:47
Normal topic ERROR: PDB reader is ignoring atom
by phanvy » Wed, 2014-04-16 17:59
2
3,798 by phanvy
Mon, 2014-04-21 03:58
Normal topic which make_fragments.pl
by renedominik » Mon, 2018-06-04 08:58
2
3,478 by renedominik
Sat, 2018-07-07 03:03
Normal topic RosettaRemodel gives no increased output when setting higher -num_trajectory
by JW_24 » Tue, 2020-09-22 11:49
2
1,717 by JW_24
Wed, 2020-09-23 01:27
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
2
1,408 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic Docking antibody to membrane protein
by Yegor_Ko » Thu, 2023-10-12 07:37
2
655 by Yegor_Ko
Fri, 2023-10-20 01:35
Normal topic Abinitio Structure Prediction - Sanity Test
by westleys » Tue, 2010-06-01 00:28
2
3,139 by westleys
Mon, 2014-04-21 06:47
Normal topic Error when clustering the output from a docking study
by jos » Thu, 2011-09-08 03:26
2
3,488 by jos
Mon, 2014-04-21 06:47
Normal topic Rosetta Resfile header
by G Mustafa » Mon, 2020-01-20 06:45
2
2,361 by G Mustafa
Tue, 2020-01-21 06:04
Normal topic score against rmsd plot of designs
by LanMei » Mon, 2022-03-21 22:46
2
1,217 by LanMei
Tue, 2022-03-22 20:45
Normal topic Talaris scoring function
by Lindsay » Sun, 2014-08-24 18:16
2
6,478 by AndrewLeaver-Fay
Sun, 2015-09-20 19:34
Normal topic what is the xxx.static.linuxgccrelease?
by syoifczeri » Sat, 2015-10-31 04:09
2
6,223 by syoifczeri
Mon, 2015-11-02 03:59
Normal topic ERROR: Not complementary at positions
by szcshr123 » Fri, 2021-02-26 05:58
2
1,974 by szcshr123
Fri, 2021-02-26 14:41
Normal topic AbinitioRelax with restraints/constraints
by jtmacd » Mon, 2011-07-11 07:07
2
4,321 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Calibur not listing cluster members
by Swillard » Sun, 2018-07-01 13:07
2
2,470 by benhardy
Fri, 2021-05-07 07:22
Normal topic FlexPepDocking.mpi.linuxgccrelease bails out ERROR: total_residue() != 0 ERROR:: Exit from: src/core/pose/Pose.cc line: 1369
by knutjbj » Thu, 2011-02-03 03:24
2
4,559 by knutjbj
Mon, 2014-04-21 06:47
Normal topic RosettaCM: threading okay, but hybridize loses many secondary structure
by lanselibai » Wed, 2021-06-23 13:51
2
1,354 by lanselibai
Thu, 2021-06-24 10:16
Normal topic Constraining a docking study
by jos » Tue, 2011-10-18 05:26
2
2,745 by rmoretti
Mon, 2014-04-21 06:47
Normal topic "Local sequence-structure compatability" in "design of ideal protein structures"
by petrikigor » Sun, 2012-12-02 09:25
2
3,237 by petrikigor
Mon, 2014-04-21 06:47
Normal topic changing the chain id
by aneamtu » Tue, 2018-01-09 00:08
2
4,966 by aneamtu
Thu, 2018-01-18 00:56
Normal topic MPI optimization on TACC stampede2 HPC
by rlwoltz » Tue, 2021-03-16 18:07
2
2,152 by rlwoltz
Wed, 2021-03-24 22:36
Normal topic ligand docking
by hong wei » Thu, 2021-11-18 05:01
2
1,409 by hong wei
Thu, 2021-11-25 02:46
Normal topic Different dG_separated from RAbD and InterfaceAnalyzer
by brubin » Mon, 2022-12-19 13:58
2
1,025 by brubin
Tue, 2022-12-20 13:26
Normal topic Using Relax to asses conformational space
by glapidoth11 » Sat, 2011-07-30 05:09
2
3,014 by smlewis
Mon, 2014-04-21 06:47
Normal topic make_fragments
by ctaylor » Mon, 2009-09-21 12:41
2
3,025 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Issue with Loop Analyzer Mover ouput
by abhi_pe_acharya » Mon, 2018-04-30 09:55
2
2,131 by abhi_pe_acharya
Mon, 2018-04-30 22:54
Normal topic how to relax structure constraining CA in Rosetta3.2?
by albumns » Tue, 2011-02-15 06:15
2
2,754 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta atoms types for enzyme design
by bharat_46010 » Thu, 2011-11-10 06:01
2
4,034 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Questions on energy oddities
by pachecoj » Wed, 2014-10-15 13:26
2
2,808 by pachecoj
Wed, 2014-10-15 15:12
Normal topic Error score_scatter_plot.py
by jrcf » Wed, 2015-12-30 05:46
2
3,511 by jrcf
Fri, 2016-02-12 16:41
Normal topic relax from a silent input file
by mintseris » Thu, 2010-04-29 19:54
2
3,083 by mintseris
Mon, 2014-04-21 06:47
Normal topic reporting IteratedConvergence status
by sdh_h » Thu, 2016-08-04 10:05
2
2,610 by sdh_h
Thu, 2016-08-04 11:22
Normal topic what is minirosetta
by Lindsay » Tue, 2012-04-10 07:48
2
9,947 by Lindsay
Mon, 2014-04-21 06:47
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