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Rosetta 3 - General

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Normal topic ERROR: beta_nov16(.wts) requested, but -corrections::beta_nov16 not set to true. This leads to a garbage scorefunction.
by sia » Mon, 2023-05-08 06:36
6
1,686 by rmoretti
Tue, 2023-05-16 07:10
Normal topic membrane ab initio error after montecarlo
by adva » Mon, 2012-12-24 01:43
6
6,244 by tevang
Mon, 2014-04-21 06:47
Normal topic Comparative Modeling databases?
by nitroamos » Wed, 2011-11-23 14:54
6
6,487 by rmoretti
Thu, 2016-04-28 16:15
Normal topic SASA packing score in Rosetta 3.1
by enoee » Wed, 2010-07-28 01:45
6
6,954 by smlewis
Mon, 2014-04-21 06:47
Normal topic Linker problems when building mini
by assaff » Mon, 2009-10-12 01:07
6
5,783 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaHoles
by ge0rgekh0ury » Mon, 2012-01-09 09:01
6
6,356 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Fixed bb design with hydrogen bond constraint
by bharat_46010 » Mon, 2012-04-30 22:56
6
6,100 by smlewis
Mon, 2014-04-21 06:47
Normal topic Relax structure using Membrane Environment Scoring Function
by anna.duncan » Thu, 2010-02-04 08:01
6
8,229 by jruhym
Mon, 2014-04-21 06:47
Normal topic How to define specific residues in alascan ?
by Park » Mon, 2011-06-13 19:56
6
7,274 by smlewis
Mon, 2014-04-21 06:47
Normal topic side-chain refinement
by qlj » Wed, 2013-02-20 04:40
6
8,979 by qlj
Mon, 2014-04-21 06:47
Normal topic Error_fragment_generation
by Payal Chatterjee » Fri, 2016-02-12 12:11
6
7,547 by G Mustafa
Fri, 2021-09-10 01:16
Normal topic ERROR: compiling rosetta3.1 with MPI
by biofisikx » Thu, 2010-08-05 16:00
6
6,644 by smlewis
Mon, 2014-04-21 06:47
Normal topic calculated ddG_bind converges to zero
by fukamitka » Mon, 2013-06-24 20:32
6
6,212 by fukamitka
Mon, 2014-04-21 06:48
Normal topic Using Patches in Rosetta
by JS » Wed, 2010-03-10 13:32
6
8,398 by JS
Mon, 2014-04-21 06:47
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43
6
5,903 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Memory leak when PDB preparation
by Jacky010 » Mon, 2019-05-06 01:28
6
4,460 by Jacky010
Tue, 2019-05-14 01:24
Normal topic AbinitioRelax under different directories without -constant_seed -jran flag
by xpzhang » Wed, 2010-09-15 14:56
6
7,756 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problem with clustering 1000 centroid pdbs
by doranhen » Sat, 2012-04-28 10:34
6
6,761 by doranhen
Mon, 2014-04-21 06:47
Normal topic Fe3p Heme Iron Unrecognized Despite Loading Hem Params
by vsjasion » Fri, 2011-09-02 10:37
6
7,773 by tigerous
Mon, 2014-04-21 06:47
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30
6
13,952 by rmoretti
Mon, 2014-04-21 06:47
Normal topic This element is not expected.
by ac.research » Fri, 2017-10-13 03:47
6
7,663 by vmulligan
Thu, 2020-07-16 23:31
Normal topic abinitiorelax: No funnel
by cno » Tue, 2010-07-27 06:14
6
5,774 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Can i start again the job ?
by byin » Thu, 2011-09-15 01:19
6
5,589 by byin
Mon, 2014-04-21 06:47
Normal topic Cannot run binaries after successful compilation
by ac.research » Mon, 2017-08-14 02:56
6
7,487 by ac.research
Fri, 2017-08-18 00:57
Normal topic NR Database Download in install_dependencies.pl (for make_fragments.pl) Broken
by Jacob_Verburgt » Tue, 2020-03-10 08:58
6
5,666 by Jacob_Verburgt
Wed, 2020-03-11 05:18
Normal topic dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.
by jyotisutar9 » Thu, 2016-12-01 00:39
6
6,368 by jyotisutar9
Wed, 2016-12-14 09:39
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
1,865 by rmoretti
Mon, 2023-02-20 16:07
Normal topic How to run Rosetta3 in parallel
by lennylv » Mon, 2009-03-30 04:21
6
10,008 by rmoretti
Mon, 2014-04-21 06:47
Normal topic distances definition in course-grained (centroid mode) steps
by allan.ferrari » Tue, 2017-01-03 05:15
6
5,514 by allan.ferrari
Tue, 2017-01-03 11:15
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
6
4,432 by jadolfbr
Thu, 2020-09-24 10:04
Normal topic What's a good application to thread a sequence over a peptide (of a peptide-protein complex) and minimize?
by brspurri » Tue, 2013-02-12 08:19
6
7,344 by smlewis
Mon, 2014-04-21 06:47
Normal topic The design of a helical peptide
by Jacob-kong » Tue, 2012-06-26 06:26
6
8,386 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic is it possible to ab initio only a part of a protein?
by albumns » Sun, 2011-02-13 08:10
6
5,113 by albumns
Mon, 2014-04-21 06:47
Normal topic Public subversion / Enzyme design public app
by weallen » Tue, 2009-08-11 20:50
6
5,692 by weallen
Mon, 2014-04-21 06:47
Normal topic pdb files in Rosetta format
by zhisheng » Mon, 2011-10-31 08:52
6
7,415 by smlewis
Mon, 2014-04-21 06:47
Normal topic Don't want to output the design structure
by Lindsay » Wed, 2012-05-02 08:02
6
5,850 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Atomic refinement with fixed ligand
by ahmadkhalifa » Tue, 2018-07-24 10:41
6
4,957 by rmoretti
Mon, 2018-08-20 11:45
Normal topic Talaris score function
by nawsad » Tue, 2013-05-21 03:32
7
9,048 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Error running Abinitio relax with @flags
by samuelrpita » Mon, 2015-10-05 13:20
7
8,101 by rmoretti
Tue, 2015-10-27 09:11
Normal topic Structure refinement guided by Cryo-EM density maps
by ahmadkhalifa » Thu, 2018-03-08 08:22
7
6,971 by ahmadkhalifa
Tue, 2018-05-01 09:04
Normal topic Docking + Active Site Design
by bharat_46010 » Sat, 2014-12-13 23:04
7
8,660 by rmoretti
Wed, 2015-01-21 08:43
Normal topic Rosetta3 Tutorials Beta Release
by smlewis » Fri, 2011-08-19 13:35
7
7,903 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
9,520 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop Modeling Deletes Residues
by Julix » Wed, 2012-09-05 10:14
7
7,025 by smlewis
Mon, 2014-04-21 06:47
Normal topic log files
by shadrinams » Fri, 2018-01-26 07:29
7
7,133 by shadrinams
Mon, 2018-02-12 11:47
Normal topic Is the packer aware of non canonical amino acids?
by krdav » Tue, 2016-08-16 08:16
7
6,684 by krdav
Wed, 2016-08-17 12:57
Normal topic about Residue Number in Rosetta
by jiongzhang » Mon, 2012-06-11 14:58
7
10,721 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to deal with Cu-as a ligand or as part of the receptor?
by hanypao » Fri, 2011-09-30 18:50
7
10,602 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Question on eval_atom_derivative function.
by Al52 » Thu, 2015-12-03 16:17
7
7,009 by rmoretti
Thu, 2016-02-04 09:29
Normal topic best_ifaceE.py error
by rosa » Fri, 2013-07-12 08:35
7
6,909 by rosa
Mon, 2014-04-21 06:48
Normal topic A question about Multiple constraints
by kxiao » Mon, 2014-06-16 07:02
7
7,495 by masterofpuppets
Fri, 2014-12-19 08:30
Normal topic Using D-amino acids in Rosetta docking
by moehle » Wed, 2011-06-01 00:49
7
8,744 by moehle
Mon, 2014-04-21 06:47
Normal topic Reproducing Rosetta++ scoring function with Rosetta 3?
by JuliusSu » Mon, 2014-03-17 21:15
7
7,507 by JuliusSu
Wed, 2014-03-19 20:38
Normal topic Antibody homology modeling fails after blastp
by sunhwan » Sat, 2017-02-18 11:25
7
6,259 by sunhwan
Mon, 2017-02-27 11:02
Normal topic How does one prevent Rosetta from connecting two separate chains?
by jhbrown » Thu, 2011-12-15 14:08
7
7,104 by Anonymous
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax using multiple cores on a single machine without mpi?
by JoG » Tue, 2011-10-25 00:40
7
11,980 by smlewis
Mon, 2014-04-21 06:47
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57
7
6,644 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to transfer the rosetta score to physical unit?
by Lindsay » Thu, 2012-06-28 09:33
7
8,226 by Lindsay
Mon, 2014-04-21 06:47
Normal topic relax structure before design?
by Lindsay » Tue, 2013-11-05 20:50
7
10,154 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Error when renumbering PDB
by dzhao » Wed, 2012-07-18 01:03
7
9,540 by rmoretti
Mon, 2014-04-21 06:47
Normal topic hydrophobicity patch
by Lindsay » Fri, 2012-05-04 08:24
7
9,432 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Rosetta (antibody_designer) performance
by Kihang _Youn » Wed, 2022-03-02 00:48
7
2,709 by Kihang _Youn
Thu, 2022-03-10 16:30
Normal topic errors while running rosetta 3.1
by isengupta13 » Tue, 2011-05-17 18:11
7
7,972 by jurkm
Mon, 2014-04-21 06:47
Normal topic ERROR READING PDB FILE
by asmi » Sat, 2011-02-26 07:23
7
9,108 by smlewis
Mon, 2014-04-21 06:47
Normal topic cutpoint error!
by monos_morpheus » Thu, 2011-04-07 08:04
7
7,910 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic rerun same experiment on MPI.
by exchhattu » Tue, 2010-02-23 21:14
7
7,215 by exchhattu
Mon, 2014-04-21 06:47
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40
7
6,490 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Rosetta3.3 enzyme_design errors
by jtmacd » Wed, 2012-01-25 03:33
7
8,168 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Help with get_pdb.py for PDB file cleaning
by lzx32 » Mon, 2011-03-28 02:11
7
9,195 by smlewis
Mon, 2014-04-21 06:47
Normal topic memory issue rosetta3.4 scripts
by ast » Mon, 2013-01-28 06:25
8
10,105 by smlewis
Mon, 2014-04-21 06:47
Normal topic loop remodelling with a fixed bound DNA
by jtmacd » Thu, 2010-02-25 03:23
8
6,741 by jtmacd
Mon, 2014-04-21 06:47
Normal topic kinematic loop modeling/sequence design keeps crashing with segmentation fault
by banshee » Thu, 2013-03-28 09:52
8
8,543 by smlewis
Mon, 2014-04-21 06:47
Normal topic Submitting job to local cluster
by tusharranjanmoharana » Fri, 2016-04-15 01:38
8
10,225 by rmoretti
Mon, 2016-05-09 09:23
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06
8
10,842 by rmoretti
Tue, 2019-07-09 12:50
Normal topic Error with non-canonical amino acid in SnugDock.
by sk0319 » Thu, 2016-12-29 16:12
8
7,542 by sk0319
Wed, 2017-01-11 10:52
Normal topic building a 77 aa long protein fragment
by tevang » Sat, 2010-02-20 11:37
8
7,716 by gsmurphy
Mon, 2014-04-21 06:47
Normal topic Problems with Cterm_amidation.txt
by helenah » Thu, 2020-10-08 04:52
8
5,419 by helenah
Tue, 2020-11-03 04:33
Normal topic Resfile
by vijayaraj81 » Thu, 2014-02-27 01:14
8
9,131 by vijayaraj81
Tue, 2014-03-04 05:07
Normal topic ETABLE constraint function type
by allan.ferrari » Tue, 2017-01-10 08:01
8
6,586 by smlewis
Sun, 2017-01-15 18:14
Normal topic talaris2013 energy terms modifications
by peony » Sat, 2013-11-23 02:48
8
17,191 by rmoretti
Mon, 2014-04-21 06:48
Normal topic RosettaVIP
by nick.polizzi » Tue, 2013-08-06 15:13
8
7,906 by rmoretti
Mon, 2014-04-21 06:48
Normal topic using constraints with AbinitioRelax (Rosetta 3.1)
by ndousis » Fri, 2009-12-18 08:56
8
8,879 by ndousis
Mon, 2014-04-21 06:47
Normal topic Every thing Ok in PC end Error on Server
by jrcf » Tue, 2016-03-22 07:21
8
8,168 by jrcf
Wed, 2016-03-23 12:16
Normal topic Rosetta3 Tutorials
by smlewis » Fri, 2011-11-18 07:33
8
17,627 by rmoretti
Tue, 2019-07-09 10:24
Normal topic can't access rosetta commercial license download via given URL from CoMotion
by y_atsmonraz » Tue, 2023-02-14 11:04
8
2,074 by rmoretti
Thu, 2023-02-16 13:48
Normal topic Rosetta job distribution error
by ss » Thu, 2019-08-01 09:26
8
5,990 by ac.research
Mon, 2020-02-10 08:19
Normal topic Debugging Rosetta under XCode
by sacch » Sun, 2011-10-16 18:23
8
8,579 by sacch
Mon, 2014-04-21 06:47
Normal topic Looking for a pdb....
by MarkW » Mon, 2014-10-13 15:45
8
8,477 by rmoretti
Mon, 2014-11-03 16:30
Normal topic Rosetta reference energy
by Lindsay » Mon, 2012-05-07 07:56
9
9,698 by Lindsay
Mon, 2014-04-21 06:47
Normal topic MPI stall
by jadolfbr » Thu, 2013-10-10 18:59
9
10,728 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic Change in binding energy after mutation in interface?
by cossio » Mon, 2014-12-01 06:27
9
11,600 by rmoretti
Thu, 2015-04-30 16:25
Normal topic flexible backbone design (fixbb+relax)
by sdh_h » Mon, 2013-02-04 03:19
9
12,188 by gsmurphy
Mon, 2014-04-21 06:47
Normal topic Running a ReportFSC mover between two .mrc maps
by ahmadkhalifa » Mon, 2018-03-12 07:52
9
6,367 by brandon.frenz
Tue, 2018-03-20 10:28
Normal topic Can Fold-and-dock protocol applied to membrane proteins
by justin » Thu, 2011-07-21 00:14
9
9,539 by wangyr
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax with very small peptides
by jamsmad » Tue, 2012-09-04 13:45
9
9,736 by jamsmad
Mon, 2014-04-21 06:47
Normal topic Clustering using an disrupted run silent file
by PaulaBanks » Mon, 2013-07-15 02:19
9
8,814 by rmoretti
Wed, 2014-09-24 09:57
Normal topic input_score_filter not taken by program cluster ?
by Anonymous » Mon, 2012-06-11 09:14
9
9,308 by attesor
Fri, 2014-10-31 04:49
Normal topic Loop Modeling with fixed backbone
by bharat_46010 » Mon, 2011-12-19 05:20
9
8,884 by bharat_46010
Mon, 2014-04-21 06:47
Normal topic is it possible to generate models without hydrogen?
by albumns » Fri, 2012-03-02 12:24
9
8,488 by albumns
Mon, 2014-04-21 06:47
Normal topic How to calculate the binding energy of peptide and a protein?
by tianbu » Thu, 2014-02-13 20:44
9
11,519 by tianbu
Mon, 2014-02-17 03:36
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