This historical page is locked! For new posts see Github Discussions.

You are here

Home » Forums » Rosetta 3

Rosetta 3 - General

Topic / Topic starter Repliessort ascending Views Last post
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 relax NOT CONVERGED
by albumns » Thu, 2010-06-24 21:25 		3
 3,435 by smlewis
Mon, 2014-04-21 06:47
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 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 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 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 Loop modeling FLAGS
by jklett » Fri, 2009-12-04 02:45 		3
 3,730 by jklett
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 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 Loop Modeling
by ctaylor » Fri, 2009-12-18 11:42 		3
 3,610 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Solving van der waals clashes in a transmembrane protein model with rosetta
by doranhen » Wed, 2012-12-05 00:12 		3
 3,909 by smlewis
Mon, 2014-04-21 06:47
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 Rosetta dock parallel
by mahajanr » Tue, 2010-06-01 16:04 		3
 4,392 by smlewis
Mon, 2014-04-21 06:47
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
 3,011 by ylwang
Wed, 2018-11-14 03:03
Normal topic "CEN" atom in the pdb file
by wszjzhang » Wed, 2010-03-17 14:35 		3
 4,938 by anusmita_sahoo
Mon, 2014-04-21 06:47
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 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 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
 3,872 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
 2,533 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 Problem creating pNNMAKE.gnu
by anirbanzz » Sat, 2010-04-17 02:14 		3
 4,233 by monica0569
Mon, 2014-04-21 06:47
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 NOE constraints with Rosetta 3.1
by mpiuzzi » Wed, 2010-02-24 02:40 		3
 3,677 by mpiuzzi
Mon, 2014-04-21 06:47
Normal topic AnchoredPDBcreator
by spraha » Wed, 2012-03-14 23:34 		3
 3,706 by smlewis
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 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 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 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 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 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 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
 4,578 by knutjbj
Mon, 2014-04-21 06:47
Normal topic loop file
by banshee » Tue, 2013-06-04 13:26 		2
 2,880 by banshee
Mon, 2014-04-21 06:48
Normal topic Score Differences between Ab Initio Scoring and Rescore
by mmarlett » Wed, 2016-06-15 09:14 		2
 2,768 by mmarlett
Thu, 2016-06-16 07:06
Normal topic Design with non-canonical amino acids (NCAA)
by yinasun » Mon, 2019-08-05 00:34 		2
 2,600 by matteoferla
Thu, 2019-08-22 05:39
Normal topic jd2 time out error
by ytao » Mon, 2013-03-04 20:47 		2
 2,828 by ytao
Mon, 2014-04-21 06:47
Normal topic Unable to download Rosetta
by Yair Tenorio » Mon, 2023-10-23 11:48 		2
 596 by Yair Tenorio
Mon, 2023-10-23 12:29
Normal topic Is CST_Design required for enzdes protocol?
by dasdevashishdas » Mon, 2018-09-03 00:51 		2
 2,452 by dasdevashishdas
Thu, 2018-09-27 03:35
Normal topic What is the best way to make a residue-specific SASA constraint?
by jmaly » Thu, 2020-01-23 16:40 		2
 2,529 by matteoferla
Wed, 2020-01-29 12:18
Normal topic problem plotting results from docking_analyser with provided Rscript
by madammolecular » Mon, 2021-02-01 14:44 		2
 1,691 by amystevens
Thu, 2021-09-30 14:18
Normal topic Weekly releases for commercial users?
by rjacak » Tue, 2022-03-22 07:48 		2
 1,332 by rjacak
Thu, 2022-03-31 10:53
Normal topic error when running beta_strand_homodimer_design
by szypanther » Sun, 2014-05-25 20:22 		2
 3,703 by szypanther
Mon, 2014-05-26 22:03
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36 		2
 2,453 by CameronJA
Wed, 2022-01-19 20:50
Normal topic activation of filters in rosetta3.0 or later
by exchhattu » Thu, 2009-12-03 17:52 		2
 2,897 by exchhattu
Mon, 2014-04-21 06:47
Normal topic I can't find the workflow about modeling disordered regsion using rosetta?
by lihowe » Thu, 2011-12-29 03:45 		2
 3,179 by wangyr
Mon, 2014-04-21 06:47
Normal topic Does the energy score output by fixbb design have unit?
by Lindsay » Mon, 2012-06-18 15:03 		2
 3,189 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Configuration of Robetta fragment libraries
by Run » Fri, 2014-01-24 23:03 		2
 3,139 by Run
Mon, 2014-04-21 06:48
Normal topic loop design
by varma » Sun, 2012-11-04 21:25 		2
 4,139 by varma
Mon, 2014-04-21 06:47
Normal topic Jump::random_trans strange behavior
by SergeyP » Tue, 2015-11-03 07:56 		2
 2,740 by SergeyP
Sat, 2015-12-19 05:20
Normal topic How to transform a pose from symmetric into non-symmetric?
by msardejani » Tue, 2016-10-04 16:55 		2
 2,697 by msardejani
Wed, 2016-10-05 10:53
Normal topic all-atom refinement with Relax application
by zwenthor » Mon, 2010-02-15 22:45 		2
 3,008 by zwenthor
Mon, 2014-04-21 06:47
Normal topic Undocumented changes in BackrubDD
by abhi_pe_acharya » Mon, 2018-07-16 00:24 		2
 2,174 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
 2,098 by dfcoelho
Tue, 2019-11-19 10:16
Normal topic how to relax structure constraining CA in Rosetta3.2?
by albumns » Tue, 2011-02-15 06:15 		2
 2,776 by smlewis
Mon, 2014-04-21 06:47
Normal topic fixbb design use
by Lindsay » Fri, 2012-03-23 09:05 		2
 2,972 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18 		2
 5,237 by pepfolder
Mon, 2014-04-21 06:47
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
 2,992 by johnnytam100
Wed, 2019-05-15 18:45
Normal topic Can't find the source code of FlexPepDock protocol in Rosetta3.1
by SunH » Thu, 2010-09-16 06:28 		2
 2,919 by barak
Mon, 2014-04-21 06:47
Normal topic The -symmetry:perturb_rigid_body_dofs flag
by doranhen » Sat, 2012-04-28 13:01 		2
 2,932 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
 3,132 by pachecoj
Thu, 2014-10-09 18:15
Normal topic Expanding the silent file
by jharamesh » Fri, 2018-01-12 09:15 		2
 2,201 by rmoretti
Mon, 2018-01-15 14:35
Normal topic Abinitio Structure Prediction - Sanity Test
by westleys » Tue, 2010-06-01 00:28 		2
 3,168 by westleys
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
 3,271 by doranhen
Mon, 2014-04-21 06:47
Normal topic sign of ddG of mutation
by Lindsay » Wed, 2013-11-27 00:25 		2
 4,848 by Lindsay
Mon, 2014-04-21 06:48
Normal topic Calculating binding affinity
by phanvy » Wed, 2014-10-15 23:35 		2
 4,783 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
 2,228 by sheehajh
Thu, 2018-02-08 21:18
Normal topic perturb_temp flag
by Loki01 » Tue, 2018-11-27 05:06 		2
 2,112 by rmoretti
Wed, 2019-04-03 09:58