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Rosetta 3 - General

Topic / Topic starter Repliessort ascending Views Last post
Normal topic ddG from backrub
by jte » Tue, 2010-10-05 14:09 		3
 3,442 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta lack of necessary application
by ylwang » Wed, 2018-11-07 01:13 		3
 2,960 by rmoretti
Wed, 2018-11-21 13:50
Normal topic Unrecognized aa NO3
by JadAbbass » Sun, 2013-07-14 10:48 		3
 4,491 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic fixbb program
by Lindsay » Tue, 2012-05-08 13:56 		3
 3,558 by AndrewLeaver-Fay
Mon, 2014-04-21 06:47
Normal topic How to use RotamerDump to access one and two-body energy tables?
by msun » Wed, 2013-01-16 12:26 		3
 3,363 by msun
Mon, 2014-04-21 06:47
Normal topic Possible Shellshock Patch problem results in no output files being written
by hazards » Wed, 2014-10-22 13:48 		3
 6,610 by rmoretti
Mon, 2014-11-03 16:39
Normal topic Bind a Ligand to RNA
by hdavis9 » Wed, 2010-07-14 09:07 		3
 3,342 by smlewis
Mon, 2014-04-21 06:47
Normal topic [dev] determine which score_type's enabled in create_energy_method?
by ipetrik_ambry » Fri, 2017-10-27 15:37 		3
 2,915 by rmoretti
Mon, 2017-10-30 12:02
Normal topic Does Rosetta have a class diagram for each class in the source code?
by ylwang » Thu, 2019-11-21 04:24 		3
 2,417 by ylwang
Sat, 2019-11-23 06:26
Normal topic loop modeling
by isengupta13 » Wed, 2011-06-01 15:00 		3
 4,043 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop modeling FLAGS
by jklett » Fri, 2009-12-04 02:45 		3
 3,730 by jklett
Mon, 2014-04-21 06:47
Normal topic what option should I use if I want to use the dfire in 3.4
by Lindsay » Thu, 2012-04-12 05:19 		3
 3,815 by smlewis
Mon, 2014-04-21 06:47
Normal topic Models which are not recorded (Abinitio protocol)
by allan.ferrari » Fri, 2015-08-28 13:39 		3
 3,681 by rmoretti
Thu, 2015-09-17 12:42
Normal topic How to integrate Rosetta code to my program?
by Lsg » Tue, 2011-06-28 07:18 		3
 4,423 by smlewis
Mon, 2014-04-21 06:47
Normal topic acceptable RMSD value in the clustered structures?
by ritacc18 » Wed, 2013-06-19 14:53 		3
 9,314 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Loop Modeling
by ctaylor » Fri, 2009-12-18 11:42 		3
 3,610 by ctaylor
Mon, 2014-04-21 06:47
Normal topic how to use rosettadesign to do mutations on protein structure
by lqzhang » Thu, 2010-03-04 07:43 		3
 4,276 by vanita
Mon, 2014-04-21 06:47
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31 		3
 3,686 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Simple FoldTree Question
by gipsonb » Wed, 2012-04-25 18:19 		3
 3,908 by gipsonb
Mon, 2014-04-21 06:47
Normal topic Comparison between two fragment pickers
by qlj » Mon, 2013-09-02 06:34 		3
 3,982 by rmoretti
Mon, 2014-04-21 06:48
Normal topic DomainAssembly Mover with constraints (using RosettaScripts)
by resiros » Wed, 2016-09-21 11:19 		3
 3,933 by rmoretti
Mon, 2016-11-14 14:21
Normal topic Peripheral membrane protein modeling
by Fukiishi » Tue, 2018-10-02 02:09 		3
 3,066 by matteoferla
Thu, 2018-10-04 01:30
Normal topic Can I thread a two chained structure in RosettaCM?
by ahmadkhalifa » Mon, 2018-01-08 09:41 		3
 3,595 by aaxx
Wed, 2019-11-06 01:44
Normal topic Rosetta-based projects using and licensing
by SergeyP » Fri, 2018-10-26 15:45 		3
 3,350 by SergeyP
Mon, 2018-11-12 09:19
Normal topic Rosetta Dock with MPI / PBS
by edpryor » Wed, 2012-09-05 11:04 		3
 6,561 by smlewis
Mon, 2014-04-21 06:47
Normal topic When does Rosetta switch from centroid to FA mode?
by MarkW » Fri, 2015-07-03 04:48 		3
 3,658 by rmoretti
Sun, 2015-07-05 14:28
Normal topic how to use backrub in rosetta3.1
by lqzhang » Mon, 2010-01-11 14:43 		3
 3,491 by smlewis
Mon, 2014-04-21 06:47
Normal topic why energy is positive?
by albumns » Tue, 2014-12-23 00:05 		3
 4,603 by rmoretti
Mon, 2015-02-09 11:21
Normal topic Quesition about Relax Mode
by crysta11 » Wed, 2009-10-21 09:57 		3
 4,024 by smlewis
Mon, 2014-04-21 06:47
Normal topic what is 05.2009 ideal coordinates
by Lindsay » Tue, 2014-09-23 20:36 		3
 3,668 by rmoretti
Mon, 2014-09-29 13:45
Normal topic Is it better to have smaller nstruct but many runs?
by Loki01 » Mon, 2018-11-19 11:50 		3
 2,703 by smlewis
Mon, 2018-11-19 13:20
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56 		3
 3,526 by smlewis
Fri, 2016-07-29 07:43
Normal topic Design constraints on pairs of residues
by SenyorDrew » Mon, 2017-10-02 07:25 		3
 3,385 by SenyorDrew
Mon, 2017-11-13 11:44
Normal topic make_fragments
by sumukh21 » Wed, 2011-02-23 09:29 		3
 3,942 by sumukh21
Mon, 2014-04-21 06:47
Normal topic Problem with HETATM entries in PDB file
by asmi » Fri, 2011-05-20 10:17 		3
 5,951 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problems with output control
by Sunyp_IM » Thu, 2017-06-22 15:30 		3
 4,221 by rmoretti
Wed, 2017-06-28 01:33
Normal topic Hydrogen bond detection and shape complementarity
by sujigeorge1979 » Fri, 2019-06-14 02:39 		3
 2,582 by sujigeorge1979
Thu, 2019-06-27 01:30
Normal topic backrub score different from calculated score
by attesor » Wed, 2014-04-09 07:34 		3
 3,901 by rmoretti
Thu, 2014-04-10 07:38
Normal topic Problem with outputing decoys in the process of AbinitioRelax
by MA » Thu, 2017-07-13 23:27 		3
 2,948 by rmoretti
Thu, 2017-08-03 08:50
Normal topic Protein folding using Monte Carlo derived techniques and implicit solvation
by hefeweizen » Tue, 2013-12-10 06:30 		3
 4,308 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Molecular oxygen
by matteoferla » Sat, 2018-02-24 06:05 		3
 3,536 by matteoferla
Mon, 2018-02-26 02:05
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26 		3
 4,865 by smlewis
Wed, 2017-11-08 12:08
Normal topic Maximum Number of Constraints
by jurkm » Fri, 2011-06-17 05:23 		3
 5,223 by jurkm
Mon, 2014-04-21 06:47
Normal topic membrane modeling error!
by wtscrystal » Wed, 2009-12-09 21:28 		3
 5,423 by arthuc01
Mon, 2014-04-21 06:47
Normal topic Biopython error in mac os x
by vinodh » Tue, 2012-06-12 12:23 		3
 4,437 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Error with simple_cycpep_predict protocol while using a native pdb file
by Florent Langenfeld » Tue, 2019-03-26 10:05 		3
 2,668 by Florent Langenfeld
Tue, 2020-09-22 03:03
Normal topic ERROR: Assertion `build_sets_[ build_set_id ].restype().has( "1HA" )` failed. ERROR:: Exit from: src/protocols/match/upstream/Pr
by alove1 » Sat, 2023-10-28 17:19 		3
 794 by alove1
Mon, 2023-10-30 13:18
Normal topic first run of abinitio in rosetta 3.2 produces an error right away
by burkheadlab » Fri, 2011-03-04 22:50 		3
 3,735 by smlewis
Mon, 2014-04-21 06:47
Normal topic Failure to find libraries during build
by NCallahan » Mon, 2010-07-26 15:41 		3
 5,297 by smlewis
Mon, 2014-04-21 06:47
Normal topic Only 430 models are generated for membrane prediction
by justin » Wed, 2010-01-06 00:04 		3
 3,757 by smlewis
Mon, 2014-04-21 06:47
Normal topic Parallel computing in RosettaDock3.1?
by xhluo » Fri, 2010-09-03 02:31 		3
 3,702 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta3.2 cluster application file-reading error
by mdyini » Wed, 2011-03-09 16:59 		3
 5,740 by smlewis
Mon, 2014-04-21 06:47
Normal topic Information about “membrane_highres_Menv_smooth.wts”
by Groros » Sun, 2011-10-02 03:59 		3
 3,971 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddg calculation
by Lindsay » Thu, 2013-09-12 10:19 		3
 6,063 by Lindsay
Mon, 2014-04-21 06:48
Normal topic Running RosettaScripts, but got an error "src/utility/options/OptionCollection.cc, line 1153, No values of the appropriate type"
by zhoubin » Sun, 2021-02-28 08:51 		3
 2,318 by zhoubin
Mon, 2021-03-01 22:11
Normal topic Solving van der waals clashes in a transmembrane protein model with rosetta
by doranhen » Wed, 2012-12-05 00:12 		3
 3,908 by smlewis
Mon, 2014-04-21 06:47
Normal topic calculate low-resolution total docking score for a input pdb
by jasnyderjr » Fri, 2015-12-11 23:08 		3
 4,020 by rmoretti
Wed, 2015-12-16 11:22
Normal topic Does Rosetta have homology modeling protocol?
by SunH » Thu, 2010-11-04 07:36 		3
 4,385 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to set up options in rosetta
by alejandro » Wed, 2011-04-06 02:08 		3
 5,216 by smlewis
Mon, 2014-04-21 06:47
Normal topic Denovo density didn't output a structure
by ahmadkhalifa » Mon, 2018-02-12 08:10 		3
 3,008 by ylwang
Wed, 2018-11-14 03:03
Normal topic obtaing pdb files
by knutjbj » Fri, 2011-02-25 11:05 		3
 3,553 by scombs
Mon, 2014-04-21 06:47
Normal topic Save silent results to individual directory by process ID
by Payne » Sat, 2022-09-24 05:23 		3
 1,257 by rmoretti
Thu, 2022-09-29 00:15
Normal topic clustering PDBs from docking
by jbujons » Wed, 2024-04-24 08:34 		3
 263 by rmoretti
Thu, 2024-06-20 13:35
Normal topic How to generate constraints of active sites from a pdb file of an enzyme
by Albert » Sun, 2013-05-26 20:07 		3
 3,871 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Change the number of residues on pdb file!
by phanvy » Tue, 2014-04-15 23:26 		3
 10,871 by rmoretti
Mon, 2015-02-09 09:09
Normal topic pmut and scoring
by ldlamini » Tue, 2021-09-14 00:46 		3
 2,300 by matteoferla
Mon, 2021-09-20 06:05
Normal topic Where is Sicdock application now? Can I find a substitute？
by JasonIsaac » Sun, 2022-11-13 03:41 		3
 1,248 by rmoretti
Mon, 2022-11-14 07:27
Normal topic -loops:refine_repack_cycles option not accepted by loopmodel.linuxgccrelease
by tsjain » Tue, 2013-02-05 18:47 		3
 4,036 by tsjain
Mon, 2014-04-21 06:47
Normal topic run Rosetta under windows prompt
by skipper » Fri, 2013-12-20 21:16 		3
 4,499 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Clarify ProteinInterfaceDesign “randomness”
by tsztain » Wed, 2019-02-27 09:41 		3
 2,530 by rmoretti
Sat, 2019-03-30 12:12
Normal topic Rotate chain
by Germanico » Sun, 2021-05-09 16:36 		3
 2,236 by danpf
Mon, 2021-05-10 10:04
Normal topic sequence_tolerance is very slow when -ms:num_packs > 1
by coomteng@gmail.com » Thu, 2016-08-25 13:17 		3
 3,453 by coomteng@gmail.com
Fri, 2016-08-26 00:01
Normal topic Binding energy calculation
by SunH » Thu, 2010-12-09 19:29 		3
 6,161 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic create a centroid file from structure or NOE list
by logandonaldson » Wed, 2013-03-20 12:23 		3
 5,222 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fastrelax energy
by Lindsay » Thu, 2014-01-16 21:04 		3
 5,185 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Rosetta Design Stalling
by Jhreed » Sun, 2016-03-06 14:38 		3
 3,536 by rmoretti
Mon, 2016-03-07 14:20
Normal topic ERROR: f.check_fold_tree
by sudhar » Mon, 2010-08-23 08:59 		3
 3,813 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta can't handle symmetric fold and dock for >10-subunit protein?
by myang » Mon, 2011-09-26 11:52 		3
 3,773 by IAndre
Mon, 2014-04-21 06:47
Normal topic Rosetta documentation
by Ashafix » Sat, 2013-08-31 06:50 		3
 5,191 by Ashafix
Mon, 2014-04-21 06:48
Normal topic Rosetta remodel on intel Xeon Phi
by pablogalazdavison » Wed, 2016-09-14 15:35 		3
 3,575 by pablogalazdavison
Thu, 2016-09-15 16:36
Normal topic Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting.
by ldx022 » Thu, 2023-03-09 17:03 		3
 1,314 by ldx022
Sat, 2023-03-11 16:53
Normal topic AnchoredPDBcreator
by spraha » Wed, 2012-03-14 23:34 		3
 3,706 by smlewis
Mon, 2014-04-21 06:47
Normal topic I got so many atoms in one residue
by ylwang » Tue, 2020-03-24 04:40 		3
 2,220 by ylwang
Tue, 2020-03-24 19:35
Normal topic Questions about rosetta fragment library ranking and fragment conformation sampling algorithm
by mdyini » Thu, 2011-05-19 17:34 		3
 4,662 by dgront
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06 		3
 3,389 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09 		3
 2,024 by matteoferla
Fri, 2021-08-20 08:37
Normal topic Explanations to membrane_abinitio options
by justin » Wed, 2010-02-10 01:14 		3
 3,397 by justin
Mon, 2014-04-21 06:47
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17 		3
 3,920 by alejandro
Mon, 2014-04-21 06:47
Normal topic RosettaDock-4.0 score term
by Zjq1998 » Wed, 2022-06-29 22:07 		3
 1,694 by ssrb
Tue, 2022-07-05 11:07
Normal topic Error Scoring Application- Illegal attempt to score
by samuelrpita » Thu, 2015-08-06 14:45 		3
 5,125 by rmoretti
Wed, 2015-08-12 15:03
Normal topic # decoys of silent
by fred » Wed, 2014-04-02 06:00 		3
 3,635 by fred
Fri, 2014-04-04 11:34
Normal topic trying to create heme.params
by einew » Mon, 2011-02-28 13:33 		3
 4,562 by einew
Mon, 2014-04-21 06:47
Normal topic Question about run FLEXPEPDOCK with 3 chain
by phanvy » Wed, 2014-07-02 08:46 		3
 3,674 by phanvy
Wed, 2014-07-02 23:32
Normal topic score_jd2.macosclangrelease No such file or directory
by ahmadkhalifa » Mon, 2017-11-27 09:26 		3
 4,118 by everyday847
Tue, 2017-11-28 13:07
Normal topic Is it CS-HM Rosetta restraint derivation i.e cm_scripts in Rosetta 3.3 bundles?
by nh_prt » Tue, 2013-03-26 12:22 		3
 3,710 by smlewis
Mon, 2014-04-21 06:47
Normal topic Abinitio isolated
by ac.research » Wed, 2018-04-04 07:36 		3
 2,765 by smlewis
Wed, 2018-04-04 10:42
Normal topic interpreting score values in silent output file after running abinitiorelax
by burkheadlab » Wed, 2011-03-09 15:42 		3
 3,666 by smlewis
Mon, 2014-04-21 06:47
Normal topic Figuring out the input flags required for this script
by jjung380 » Wed, 2023-04-19 14:17 		3
 1,208 by rmoretti
Mon, 2023-05-15 15:23
Normal topic I am a beginner in rosetta software and need help to build params file
by nais » Fri, 2011-03-18 13:37 		3
 7,088 by rmoretti
Mon, 2014-04-21 06:47
Normal topic relax - P6G molecule
by allan.ferrari » Wed, 2016-11-30 05:01 		3
 3,216 by allan.ferrari
Tue, 2017-01-03 05:02