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Rosetta 3 - General

Topic / Topic starter Repliessort descending Views Last post
Normal topic pdb 2 silent with ss information
by kalabharath » Sun, 2013-04-14 20:59 		1
 2,548 by smlewis
Mon, 2014-04-21 06:47
Normal topic non-canonical residues parametrisation
by DmitriiN » Tue, 2016-04-05 02:37 		1
 2,169 by rmoretti
Fri, 2016-04-08 08:43
Normal topic Library of unnatural amino acid parameters
by saxen » Mon, 2017-04-17 11:08 		1
 3,898 by smlewis
Tue, 2017-04-18 08:33
Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06 		1
 1,090 by lanselibai
Wed, 2021-06-23 14:53
Normal topic PDB weird to PDB rosetta friendly
by jpfuenzalidawx » Fri, 2022-09-02 04:43 		1
 921 by rmoretti
Tue, 2022-09-06 08:13
Normal topic Filters saying atom type does not exist on residue
by mdm95 » Mon, 2024-03-04 15:13 		1
 353 by mdm95
Tue, 2024-03-05 14:05
Normal topic docking using rosetta3.1 and rosetta2.3 leads to very different results
by lqzhang » Thu, 2010-01-14 11:54 		1
 2,197 by sid
Mon, 2014-04-21 06:47
Normal topic null rosetta energy/score
by fred » Tue, 2011-10-18 10:31 		1
 2,239 by fred
Mon, 2014-04-21 06:47
Normal topic which modules support MPI now?
by albumns » Fri, 2013-11-08 01:32 		1
 2,267 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Consistent XYZvector length() zero failure in EnzDes
by mwfranklin » Thu, 2018-11-01 12:44 		1
 1,778 by rmoretti
Wed, 2018-11-21 14:14
Normal topic ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)
by Ken » Mon, 2022-05-23 07:16 		1
 841 by ajasja
Mon, 2022-05-23 07:19
Normal topic how same random seeds can be used in rosetta for mpi run.
by exchhattu » Wed, 2009-10-28 22:09 		1
 2,865 by smlewis
Mon, 2014-04-21 06:47
Normal topic Snugdock and antibody modelling
by sudhar » Thu, 2010-06-10 08:13 		1
 2,594 by smlewis
Mon, 2014-04-21 06:47
Normal topic Building Rosetta Problem: Processor architecture unsupported?
by jalfaro » Tue, 2010-03-23 05:48 		1
 3,014 by reddybg
Mon, 2014-04-21 06:47
Normal topic Pairwise decomposable terms in the Rosetta energy function
by pgainza » Wed, 2011-08-03 12:26 		1
 3,605 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44 		1
 2,198 by rmoretti
Wed, 2015-02-18 09:19
Normal topic Some problems with the "advanced protein-protein docking" tutorial
by Sunyp_IM » Tue, 2017-06-27 09:33 		1
 2,009 by smlewis
Wed, 2017-06-28 06:59
Normal topic IS there any source code about protein structure prediction with only sequences information?
by ylwang » Mon, 2019-07-08 02:36 		1
 1,650 by rmoretti
Mon, 2019-07-08 08:05
Normal topic Extracting a part of a silent file as another silent file
by almeida85 » Wed, 2021-07-28 23:53 		1
 1,286 by zivben
Sat, 2021-07-31 08:16
Normal topic Discrepancies between Foldit fa_rep score and Rosseta jd2 score fa_rep score
by mrosam » Fri, 2024-04-19 07:57 		1
 207 by rmoretti
Thu, 2024-06-20 13:38
Normal topic Running Backrub
by enoee » Wed, 2010-10-27 07:51 		1
 2,313 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Tue, 2016-01-05 09:39 		1
 2,555 by achambe
Wed, 2016-01-13 10:46
Normal topic How to judge docking success for two proteins without knowledge of native structure
by jasnyderjr » Fri, 2015-07-10 14:27 		1
 2,798 by rmoretti
Tue, 2015-07-14 15:27
Normal topic snugdock and rosetta 3.2??
by sudhar » Thu, 2011-02-24 00:36 		1
 2,336 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddG backbone movement
by dave » Wed, 2012-10-03 03:23 		2
 3,174 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
 2,390 by dasdevashishdas
Thu, 2018-08-23 18:02
Normal topic Rosetta forcefield terms and interpretation
by zigeuner » Sat, 2013-05-25 16:59 		2
 5,103 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
 4,576 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
 3,619 by rmoretti
Thu, 2018-06-28 14:09
Normal topic 4mer 6mer fragment database
by bjharris » Wed, 2020-09-09 15:12 		2
 1,902 by bjharris
Wed, 2020-09-09 20:04
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48 		2
 1,591 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
 1,065 by Liviu Copoiu
Tue, 2022-11-08 10:43
Normal topic Run PackRotamersMover on specified rotamer set
by pachecoj » Mon, 2014-11-10 06:51 		2
 2,977 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
 2,121 by Jacob_Verburgt
Tue, 2020-06-02 10:26
Normal topic Output and Input Tutorial
by jgustat » Fri, 2022-07-01 13:07 		2
 1,124 by jgustat
Fri, 2022-07-01 13:26
Normal topic Running time of Rosetta/FlexPepDock
by gerdos » Thu, 2015-10-15 02:14 		2
 2,834 by gerdos
Fri, 2015-10-16 03:01
Normal topic Job Distribution Error
by ac.research » Mon, 2020-02-10 08:22 		2
 2,150 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
 1,001 by rmoretti
Tue, 2023-03-07 08:18
Normal topic I got the message "ERROR: Residue names must be unique!".
by monos_morpheus » Sun, 2011-02-06 03:55 		2
 3,784 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic Loop modelling,
by berk » Sat, 2013-06-08 08:29 		2
 2,944 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
 3,228 by pitmand
Tue, 2015-05-26 12:20
Normal topic Clustering Rosetta output PDB files
by ritacc18 » Sat, 2014-01-11 20:13 		2
 5,826 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
 3,898 by cossio
Wed, 2014-12-03 14:51
Normal topic scoring with omega energy term
by SergeyP » Thu, 2017-03-09 12:03 		2
 2,801 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
 618 by bdh81
Sun, 2023-11-05 16:04
Normal topic Rigid Body & Flexible Minimization
by Hanieh » Thu, 2014-02-06 12:37 		2
 4,084 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
 4,518 by mgrom92
Wed, 2016-03-23 16:45
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32 		2
 1,140 by Ken
Wed, 2022-08-17 08:04
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36 		2
 2,735 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Rosetta numbering with missing occupancies
by ShaneOConnor » Fri, 2011-10-07 16:18 		2
 3,700 by ShaneOConnor
Mon, 2014-04-21 06:47
Normal topic RASREC - finding lowest energy structure
by Lati » Fri, 2015-11-20 03:08 		2
 2,994 by Lati
Tue, 2016-01-12 13:28
Normal topic DockingProtocol mover ensemble error
by dfcoelho » Tue, 2018-10-16 08:32 		2
 2,736 by brspurri
Thu, 2020-08-20 13:22
Normal topic Using mode=profile
by Biokhar » Fri, 2012-07-06 00:29 		2
 3,912 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
 2,980 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
 2,732 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
 3,394 by asbelx
Thu, 2018-04-26 00:23
Normal topic Controlling Input in the Tutorial
by Smbat » Wed, 2020-07-29 22:41 		2
 1,793 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
 1,387 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
 3,159 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
 2,870 by htorres
Mon, 2018-02-05 06:53
Normal topic de novo protein prediction
by pci112 » Tue, 2021-03-23 10:13 		2
 1,650 by pci112
Thu, 2021-03-25 01:44
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37 		2
 3,696 by smlewis
Mon, 2014-04-21 06:47
Normal topic Does Rosetta have a separate refinement function?
by ylwang » Tue, 2019-09-24 19:08 		2
 2,101 by ylwang
Tue, 2019-10-08 18:34
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04 		2
 3,805 by smlewis
Mon, 2014-04-21 06:47
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11 		2
 3,263 by Trentage
Mon, 2014-04-21 06:47
Normal topic Patches for post-translational modifications
by ltrabuco » Tue, 2011-02-22 01:00 		2
 4,210 by ltrabuco
Mon, 2014-04-21 06:47
Normal topic Is the Fold&Dock protocol availabe in Rosetta3.1
by justin » Mon, 2011-01-17 02:41 		2
 2,606 by smlewis
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
 2,747 by Karol
Thu, 2016-05-12 07:58
Normal topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:18 		2
 2,287 by jalan
Sun, 2020-04-12 08:01
Normal topic Residue variant types and fragments
by jadolfbr » Mon, 2013-01-21 09:01 		2
 3,367 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
 3,450 by smlewis
Thu, 2016-01-14 08:19
Normal topic Error in flex ddG tutorial
by wentlewi » Sat, 2020-05-16 08:06 		2
 2,027 by Alvin Yang
Wed, 2023-10-04 03:34
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57 		2
 2,668 by smlewis
Mon, 2014-04-21 06:47
Normal topic De novo backbone trace from fragments
by Victor Tobiasson » Tue, 2020-12-22 06:34 		2
 2,081 by Victor Tobiasson
Tue, 2020-12-22 09:18
Normal topic Error when clustering the output from a docking study
by jos » Thu, 2011-09-08 03:26 		2
 3,514 by jos
Mon, 2014-04-21 06:47
Normal topic Rosetta Resfile header
by G Mustafa » Mon, 2020-01-20 06:45 		2
 2,398 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
 1,249 by LanMei
Tue, 2022-03-22 20:45
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59 		2
 3,758 by biofisikx
Mon, 2014-04-21 06:47
Normal topic ERROR: PDB reader is ignoring atom
by phanvy » Wed, 2014-04-16 17:59 		2
 3,829 by phanvy
Mon, 2014-04-21 03:58
Normal topic which make_fragments.pl
by renedominik » Mon, 2018-06-04 08:58 		2
 3,513 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
 1,744 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
 1,435 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
 694 by Yegor_Ko
Fri, 2023-10-20 01:35
Normal topic Talaris scoring function
by Lindsay » Sun, 2014-08-24 18:16 		2
 6,515 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
 6,265 by syoifczeri
Mon, 2015-11-02 03:59
Normal topic ERROR: Not complementary at positions
by szcshr123 » Fri, 2021-02-26 05:58 		2
 1,999 by szcshr123
Fri, 2021-02-26 14:41
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44 		2
 2,666 by ndousis
Mon, 2014-04-21 06:47
Normal topic Modelling Sheets
by monteirotorres » Thu, 2009-07-02 11:41 		2
 2,976 by monteirotorres
Mon, 2014-04-21 06:47
Normal topic runtime error
by exchhattu » Wed, 2010-03-03 02:54 		2
 2,647 by exchhattu
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax with restraints/constraints
by jtmacd » Mon, 2011-07-11 07:07 		2
 4,360 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Calibur not listing cluster members
by Swillard » Sun, 2018-07-01 13:07 		2
 2,499 by benhardy
Fri, 2021-05-07 07:22
Normal topic RosettaCM: threading okay, but hybridize loses many secondary structure
by lanselibai » Wed, 2021-06-23 13:51 		2
 1,383 by lanselibai
Thu, 2021-06-24 10:16
Normal topic Constraining a docking study
by jos » Tue, 2011-10-18 05:26 		2
 2,766 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
 3,277 by petrikigor
Mon, 2014-04-21 06:47
Normal topic changing the chain id
by aneamtu » Tue, 2018-01-09 00:08 		2
 4,995 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
 2,184 by rlwoltz
Wed, 2021-03-24 22:36
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06 		2
 3,563 by vanita
Mon, 2014-04-21 06:47
Normal topic rosetta run error
by isengupta13 » Thu, 2010-06-03 19:00 		2
 3,242 by aminzia
Fri, 2019-07-26 13:14
Normal topic ligand docking
by hong wei » Thu, 2021-11-18 05:01 		2
 1,432 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
 1,066 by brubin
Tue, 2022-12-20 13:26