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Rosetta 3 - General

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Normal topic Cluster application, How does it sort decoys by energy?
by Apiwat » Wed, 2014-04-16 01:52
2
2,273 by Apiwat
Thu, 2014-04-17 09:56
Normal topic possible idealize app bug - residues being deleted
by jtmacd » Mon, 2009-06-08 06:27
2
2,121 by jtmacd
Mon, 2014-04-21 06:47
Normal topic "caught exception" for PDB with membrane "DUM" residues
by nitroamos » Wed, 2018-05-30 08:35
2
2,684 by Awagner7
Tue, 2020-04-28 10:51
Normal topic Can't find the source code of FlexPepDock protocol in Rosetta3.1
by SunH » Thu, 2010-09-16 06:28
2
2,249 by barak
Mon, 2014-04-21 06:47
Normal topic Creation of core.* file in current running directory
by alejandro » Tue, 2011-12-06 06:19
2
2,525 by alejandro
Mon, 2014-04-21 06:47
Normal topic Multigraft
by bo » Tue, 2013-12-24 18:06
2
2,549 by Sergey Menis
Mon, 2014-04-21 06:48
Normal topic Meaning of a couple terms?
by aloshbau » Sun, 2016-02-07 16:48
2
1,865 by aloshbau
Sun, 2016-02-14 20:14
Normal topic Rosetta Double changing mmCIF chain ID
by Victor Tobiasson » Thu, 2021-05-13 07:57
2
736 by Victor Tobiasson
Thu, 2021-05-13 08:33
Normal topic Connecting 2 Domains Via Non-Flexible Linker
by jurkm » Mon, 2011-09-05 06:10
2
4,826 by kbuhr
Tue, 2015-07-14 04:30
Normal topic how to relax structure constraining CA in Rosetta3.2?
by albumns » Tue, 2011-02-15 06:15
2
2,064 by smlewis
Mon, 2014-04-21 06:47
Normal topic Symmetric Processing for evaluating side-chain of chi angle
by qlj » Wed, 2012-10-10 04:08
2
2,336 by smlewis
Mon, 2014-04-21 06:47
Normal topic minimum number of nstruct to build at 65% homolgy
by MRH » Thu, 2013-08-22 07:29
2
2,303 by MRH
Mon, 2014-04-21 06:48
Normal topic Working through tutorials: expected output scorces differ from calculated results
by j.schmue » Sat, 2020-01-18 13:16
2
1,098 by j.schmue
Tue, 2020-01-28 13:31
Normal topic build parallel version of Rosetta
by atfrank » Tue, 2009-10-06 22:33
2
3,087 by smlewis
Mon, 2014-04-21 06:47
Normal topic error--rosetta fragment‐based refinement protocol for refinement against EM density
by gsuchunli » Thu, 2016-06-30 11:06
2
3,158 by rmoretti
Tue, 2016-07-12 08:18
Normal topic is there a preferred way to enforce an hydrogen bond ?
by logandonaldson » Wed, 2013-03-20 13:14
2
2,192 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Fragment picker
by phanvy » Mon, 2014-12-08 04:25
2
2,468 by phanvy
Wed, 2014-12-10 00:17
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41
2
2,077 by rmoretti
Mon, 2016-03-14 07:58
Normal topic Data Check for a newb
by ac.research » Sun, 2017-03-12 23:42
2
1,738 by ac.research
Fri, 2017-03-31 07:36
Normal topic Having trouble producing a .pdb file from a silent output file after running abinitio relax
by burkheadlab » Wed, 2011-03-09 12:48
2
2,372 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic Adding noncanonical amino acid (PCA) to Rosetta 3
by JuliusSu » Fri, 2014-08-01 11:23
2
3,240 by JuliusSu
Fri, 2014-08-08 02:07
Normal topic Rosetta Dock with MPI / PBS
by edpryor » Wed, 2012-09-05 11:04
3
5,461 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
2,750 by rmoretti
Sun, 2015-07-05 14:28
Normal topic why energy is positive?
by albumns » Tue, 2014-12-23 00:05
3
3,471 by rmoretti
Mon, 2015-02-09 11:21
Normal topic what is 05.2009 ideal coordinates
by Lindsay » Tue, 2014-09-23 20:36
3
2,688 by rmoretti
Mon, 2014-09-29 13:45
Normal topic Can I thread a two chained structure in RosettaCM?
by ahmadkhalifa » Mon, 2018-01-08 09:41
3
2,473 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
2,193 by SergeyP
Mon, 2018-11-12 09:19
Normal topic Is it better to have smaller nstruct but many runs?
by Loki01 » Mon, 2018-11-19 11:50
3
1,699 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
2,557 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
2,358 by SenyorDrew
Mon, 2017-11-13 11:44
Normal topic Problem with HETATM entries in PDB file
by asmi » Fri, 2011-05-20 10:17
3
4,679 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problems with output control
by Sunyp_IM » Thu, 2017-06-22 15:30
3
2,786 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
1,630 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
2,871 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
1,992 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
3,261 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Molecular oxygen
by matteoferla » Sat, 2018-02-24 06:05
3
2,318 by matteoferla
Mon, 2018-02-26 02:05
Normal topic Loop modeling FLAGS
by jklett » Fri, 2009-12-04 02:45
3
2,674 by jklett
Mon, 2014-04-21 06:47
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
3,042 by smlewis
Wed, 2017-11-08 12:08
Normal topic why docking results are different?
by albumns » Sat, 2010-12-18 23:53
3
2,780 by smlewis
Mon, 2014-04-21 06:47
Normal topic Maximum Number of Constraints
by jurkm » Fri, 2011-06-17 05:23
3
4,245 by jurkm
Mon, 2014-04-21 06:47
Normal topic is it possbile to cluster pdb files?
by albumns » Wed, 2010-10-06 02:38
3
4,395 by smlewis
Mon, 2014-04-21 06:47
Normal topic Biopython error in mac os x
by vinodh » Tue, 2012-06-12 12:23
3
3,404 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
1,615 by Florent Langenfeld
Tue, 2020-09-22 03:03
Normal topic Loop Modeling
by ctaylor » Fri, 2009-12-18 11:42
3
2,636 by ctaylor
Mon, 2014-04-21 06:47
Normal topic first run of abinitio in rosetta 3.2 produces an error right away
by burkheadlab » Fri, 2011-03-04 22:50
3
2,931 by smlewis
Mon, 2014-04-21 06:47
Normal topic Quesition about Relax Mode
by crysta11 » Wed, 2009-10-21 09:57
3
2,871 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to use backrub in rosetta3.1
by lqzhang » Mon, 2010-01-11 14:43
3
2,631 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
4,754 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
3,106 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddg calculation
by Lindsay » Thu, 2013-09-12 10:19
3
4,616 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
915 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
2,988 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
2,982 by rmoretti
Wed, 2015-12-16 11:22
Normal topic Determine the weights of score functions
by SunH » Thu, 2010-09-02 07:20
3
3,698 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
4,155 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
1,998 by ylwang
Wed, 2018-11-14 03:03
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
2,913 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
8,457 by rmoretti
Mon, 2015-02-09 09:09
Normal topic pmut and scoring
by ldlamini » Tue, 2021-09-14 00:46
3
749 by matteoferla
Mon, 2021-09-20 06:05
Normal topic Bind a Ligand to RNA
by hdavis9 » Wed, 2010-07-14 09:07
3
2,489 by smlewis
Mon, 2014-04-21 06:47
Normal topic -loops:refine_repack_cycles option not accepted by loopmodel.linuxgccrelease
by tsjain » Tue, 2013-02-05 18:47
3
3,045 by tsjain
Mon, 2014-04-21 06:47
Normal topic run Rosetta under windows prompt
by skipper » Fri, 2013-12-20 21:16
3
3,571 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Clarify ProteinInterfaceDesign “randomness”
by tsztain » Wed, 2019-02-27 09:41
3
1,544 by rmoretti
Sat, 2019-03-30 12:12
Normal topic Rotate chain
by Germanico » Sun, 2021-05-09 16:36
3
939 by danpf
Mon, 2021-05-10 10:04
Normal topic membrane modeling error!
by wtscrystal » Wed, 2009-12-09 21:28
3
4,344 by arthuc01
Mon, 2014-04-21 06:47
Normal topic sequence_tolerance is very slow when -ms:num_packs > 1
by coomteng@gmail.com » Thu, 2016-08-25 13:17
3
2,470 by coomteng@gmail.com
Fri, 2016-08-26 00:01
Normal topic does rosetta good at peptide-protein docking?
by albumns » Mon, 2010-12-27 18:51
3
4,500 by smlewis
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
4,265 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fastrelax energy
by Lindsay » Thu, 2014-01-16 21:04
3
4,036 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Rosetta Design Stalling
by Jhreed » Sun, 2016-03-06 14:38
3
2,488 by rmoretti
Mon, 2016-03-07 14:20
Normal topic Only 430 models are generated for membrane prediction
by justin » Wed, 2010-01-06 00:04
3
2,760 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
2,978 by IAndre
Mon, 2014-04-21 06:47
Normal topic Rosetta documentation
by Ashafix » Sat, 2013-08-31 06:50
3
4,185 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
2,542 by pablogalazdavison
Thu, 2016-09-15 16:36
Normal topic how to use rosettadesign to do mutations on protein structure
by lqzhang » Thu, 2010-03-04 07:43
3
3,419 by vanita
Mon, 2014-04-21 06:47
Normal topic AnchoredPDBcreator
by spraha » Wed, 2012-03-14 23:34
3
2,677 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
1,265 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
3,828 by dgront
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06
3
1,908 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
725 by matteoferla
Fri, 2021-08-20 08:37
Normal topic how to get reliable results for carbohydrate docking?
by albumns » Sun, 2010-09-05 23:12
3
4,136 by smlewis
Mon, 2014-04-21 06:47
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17
3
3,073 by alejandro
Mon, 2014-04-21 06:47
Normal topic Error Scoring Application- Illegal attempt to score
by samuelrpita » Thu, 2015-08-06 14:45
3
3,676 by rmoretti
Wed, 2015-08-12 15:03
Normal topic # decoys of silent
by fred » Wed, 2014-04-02 06:00
3
2,626 by fred
Fri, 2014-04-04 11:34
Normal topic ddG from backrub
by jte » Tue, 2010-10-05 14:09
3
2,602 by smlewis
Mon, 2014-04-21 06:47
Normal topic trying to create heme.params
by einew » Mon, 2011-02-28 13:33
3
3,550 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
2,729 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
2,638 by everyday847
Tue, 2017-11-28 13:07
Normal topic Failure to find libraries during build
by NCallahan » Mon, 2010-07-26 15:41
3
4,352 by smlewis
Mon, 2014-04-21 06:47
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
2,805 by smlewis
Mon, 2014-04-21 06:47
Normal topic Abinitio isolated
by ac.research » Wed, 2018-04-04 07:36
3
1,735 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
2,804 by smlewis
Mon, 2014-04-21 06:47
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
5,888 by rmoretti
Mon, 2014-04-21 06:47
Normal topic relax - P6G molecule
by allan.ferrari » Wed, 2016-11-30 05:01
3
2,243 by allan.ferrari
Tue, 2017-01-03 05:02
Normal topic small molecule charge generated by molfile_to_params.py
by rohi » Wed, 2021-03-17 09:35
3
909 by rmoretti
Wed, 2021-03-17 13:52
Normal topic Does Rosetta have an app for detecting brakes and clashes in proteins
by Anatol » Sat, 2012-09-08 15:48
3
3,574 by smlewis
Mon, 2014-04-21 06:47
Normal topic Refinement of a PDB structure containing multiple models
by ahmadkhalifa » Wed, 2018-04-18 07:44
3
1,867 by smlewis
Wed, 2018-04-18 19:03
Normal topic ERROR: unrecognized atomtype property VIRTUAL
by harshkhare » Mon, 2011-11-14 09:40
3
3,062 by harshkhare
Mon, 2014-04-21 06:47
Normal topic Propagating the same mutation over "different" chains
by mdeklotz » Thu, 2018-07-26 09:27
3
1,783 by rmoretti
Fri, 2018-08-03 08:42
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