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Rosetta 3 - General

Topic / Topic starter Repliessort descending Views Last post
Normal topic pro_closure energy scoring function
by peony » Sat, 2013-11-16 13:22
5
5,190 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Error when using RabD with a nanobody.
by zhangying1990 » Mon, 2018-12-17 04:40
5
3,220 by jadolfbr
Mon, 2019-01-28 08:46
Normal topic loop modelling error on Rosetta3.2 or Rosetta3.3
by exchhattu » Thu, 2011-09-29 03:58
5
4,438 by rpache
Mon, 2014-04-21 06:47
Normal topic de novo RNA loop
by c.ocasion » Sun, 2021-02-14 18:34
5
1,925 by everyday847
Mon, 2021-03-29 20:19
Normal topic Access sigma values for rotamers
by pachecoj » Thu, 2014-05-15 07:10
5
4,759 by rmoretti
Sat, 2014-05-17 14:10
Normal topic Chain specific flags
by helenah » Mon, 2020-10-19 03:31
5
2,167 by rmoretti
Fri, 2020-11-06 08:04
Normal topic rosetta_scripts_BOGUS coords warning message
by Karol » Tue, 2016-12-13 02:35
5
4,581 by Karol
Thu, 2016-12-15 01:35
Normal topic Problem with undetected lower and upper terminus variants for new polymer
by Martin Floor » Sat, 2022-06-11 06:51
5
843 by matteoferla
Fri, 2022-07-01 13:49
Normal topic Abinitio Calculations - typical parameters
by vamsi » Thu, 2010-11-11 07:06
5
5,191 by smlewis
Mon, 2014-04-21 06:47
Normal topic match_dspos1 and other matcher options
by petrikigor » Sat, 2012-10-20 09:22
5
4,805 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problems with disulphide bonds during KIC
by Loki01 » Tue, 2017-11-28 03:11
5
3,549 by Loki01
Thu, 2017-12-14 06:20
Normal topic Rotate MOVER
by gw » Wed, 2012-08-15 12:09
5
4,693 by glemmon
Mon, 2014-04-21 06:47
Normal topic protein binding energy problem
by Lindsay » Thu, 2014-04-17 23:10
5
5,065 by jadolfbr
Mon, 2014-04-21 07:30
Normal topic Error when running "plot_LHOC.py"
by Sunyp_IM » Sun, 2017-08-13 05:54
5
3,518 by smlewis
Wed, 2017-08-16 08:30
Normal topic comparison of energy
by sdh » Mon, 2010-08-16 07:55
5
4,630 by smlewis
Mon, 2014-04-21 06:47
Normal topic P-P docking with ambiguous constraints
by Anouk » Fri, 2013-11-08 11:38
5
5,889 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Rotamer Library Generation in Rosetta3
by jcminerlanl » Wed, 2016-11-30 07:34
5
4,793 by rmoretti
Tue, 2021-02-09 11:52
Normal topic BridgeChainsMover
by msardejani » Sun, 2016-08-07 17:32
5
4,247 by smlewis
Tue, 2016-08-30 13:47
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33
5
4,525 by rmoretti
Tue, 2014-11-18 10:01
Normal topic Typical relax options not applied in relax.mpi.linuxiccrelease??
by David Weis » Mon, 2017-02-27 11:35
5
3,954 by rmoretti
Thu, 2017-08-03 09:01
Normal topic Rosetta-foldtree and docking
by tingting » Tue, 2022-03-15 22:49
5
929 by aastha.pal
Mon, 2022-06-27 09:55
Normal topic Relax command for docking purposes and cluster_vs_rmsd command
by Rkfoury » Wed, 2015-04-01 08:48
5
4,919 by rmoretti
Sat, 2015-04-25 10:05
Normal topic Secondary Structure Relax
by ac.research » Sat, 2018-03-17 10:50
5
3,642 by smlewis
Wed, 2018-03-21 08:42
Normal topic Using 2 non-standard residues in one run
by einew » Tue, 2011-03-08 21:24
5
5,762 by einew
Mon, 2014-04-21 06:47
Normal topic Evaluating energies on non-standard rotamer set
by pachecoj » Sat, 2014-07-26 16:27
5
4,260 by pachecoj
Sat, 2014-08-09 06:33
Normal topic Efficient implementation of MPI with protein design programs
by zachdebruine » Thu, 2018-06-28 10:41
5
3,531 by smlewis
Tue, 2018-07-03 11:22
Normal topic P(Res | phi,psi )
by jadolfbr » Thu, 2011-07-21 08:49
5
4,265 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic RosettaMatch
by jtmacd » Wed, 2012-01-11 06:50
5
8,826 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Suppress printing to STDOUT for applications
by tylerborrman » Tue, 2015-11-24 11:37
5
4,643 by code_Monkey
Thu, 2021-03-18 08:03
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
5,687 by smlewis
Mon, 2014-04-21 06:47
Normal topic optH flag makes hydrogen bond energy scores worse...
by tsjain » Fri, 2012-07-13 14:04
6
5,929 by smlewis
Mon, 2014-04-21 06:47
Normal topic selecting pivot_residue in Backrub for ensemble generation
by rohi » Fri, 2020-08-07 15:41
6
2,980 by matteoferla
Tue, 2020-08-11 10:00
Normal topic Native gives higher (positive) than lowest energy and clustered decoys
by tiagogomes89 » Thu, 2011-06-02 07:19
6
4,847 by rmoretti
Mon, 2014-04-21 06:47
Normal topic abinitiorelax: No funnel
by cno » Tue, 2010-07-27 06:14
6
4,770 by biofisikx
Mon, 2014-04-21 06:47
Normal topic How to run Rosetta3 in parallel
by lennylv » Mon, 2009-03-30 04:21
6
8,621 by rmoretti
Mon, 2014-04-21 06:47
Normal topic membrane ab initio error after montecarlo
by adva » Mon, 2012-12-24 01:43
6
5,304 by tevang
Mon, 2014-04-21 06:47
Normal topic Comparative Modeling databases?
by nitroamos » Wed, 2011-11-23 14:54
6
5,511 by rmoretti
Thu, 2016-04-28 16:15
Normal topic Public subversion / Enzyme design public app
by weallen » Tue, 2009-08-11 20:50
6
4,647 by weallen
Mon, 2014-04-21 06:47
Normal topic RosettaHoles
by ge0rgekh0ury » Mon, 2012-01-09 09:01
6
5,399 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
5,259 by smlewis
Mon, 2014-04-21 06:47
Normal topic side-chain refinement
by qlj » Wed, 2013-02-20 04:40
6
7,756 by qlj
Mon, 2014-04-21 06:47
Normal topic Error_fragment_generation
by Payal Chatterjee » Fri, 2016-02-12 12:11
6
5,703 by G Mustafa
Fri, 2021-09-10 01:16
Normal topic How to define specific residues in alascan ?
by Park » Mon, 2011-06-13 19:56
6
6,342 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
5,189 by fukamitka
Mon, 2014-04-21 06:48
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43
6
4,732 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Memory leak when PDB preparation
by Jacky010 » Mon, 2019-05-06 01:28
6
3,302 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
6,752 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
5,924 by doranhen
Mon, 2014-04-21 06:47
Normal topic This element is not expected.
by ac.research » Fri, 2017-10-13 03:47
6
5,981 by vmulligan
Thu, 2020-07-16 23:31
Normal topic Fe3p Heme Iron Unrecognized Despite Loading Hem Params
by vsjasion » Fri, 2011-09-02 10:37
6
6,813 by tigerous
Mon, 2014-04-21 06:47
Normal topic modeling loops between domains
by dhorita » Thu, 2009-03-05 14:48
6
4,873 by jarod
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
12,411 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Can i start again the job ?
by byin » Thu, 2011-09-15 01:19
6
4,686 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
6,038 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
4,040 by Jacob_Verburgt
Wed, 2020-03-11 05:18
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
346 by rmoretti
Mon, 2023-02-20 16:07
Normal topic dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.
by jyotisutar9 » Thu, 2016-12-01 00:39
6
4,742 by jyotisutar9
Wed, 2016-12-14 09:39
Normal topic distances definition in course-grained (centroid mode) steps
by allan.ferrari » Tue, 2017-01-03 05:15
6
4,439 by allan.ferrari
Tue, 2017-01-03 11:15
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
6,393 by smlewis
Mon, 2014-04-21 06:47
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
6
2,933 by jadolfbr
Thu, 2020-09-24 10:04
Normal topic is it possible to ab initio only a part of a protein?
by albumns » Sun, 2011-02-13 08:10
6
4,151 by albumns
Mon, 2014-04-21 06:47
Normal topic The design of a helical peptide
by Jacob-kong » Tue, 2012-06-26 06:26
6
7,327 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic Atomic refinement with fixed ligand
by ahmadkhalifa » Tue, 2018-07-24 10:41
6
3,814 by rmoretti
Mon, 2018-08-20 11:45
Normal topic pdb files in Rosetta format
by zhisheng » Mon, 2011-10-31 08:52
6
6,431 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
4,945 by Anonymous
Mon, 2014-04-21 06:47
Normal topic No score.sc generated after running flexpepdock.
by monos_morpheus » Sun, 2011-04-10 04:06
6
5,395 by robren
Mon, 2014-04-21 06:47
Normal topic Rosetta CM incorrect threading
by ahmadkhalifa » Mon, 2018-08-06 11:09
6
4,064 by rmoretti
Fri, 2018-08-24 11:59
Normal topic Problem With Rosetta3.3 Comparative/Loop Modeling And Constraints
by jurkm » Mon, 2011-09-12 01:01
6
5,466 by jurkm
Mon, 2014-04-21 06:47
Normal topic SASA packing score in Rosetta 3.1
by enoee » Wed, 2010-07-28 01:45
6
5,974 by smlewis
Mon, 2014-04-21 06:47
Normal topic Linker problems when building mini
by assaff » Mon, 2009-10-12 01:07
6
4,627 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta CM - Ignore Sporadic Errors
by Swillard » Wed, 2018-06-13 05:47
6
3,645 by rmoretti
Mon, 2018-11-12 14:29
Normal topic '-norepack_disulf' flag NOT work in Ligand-protein docking ?
by darlintai » Tue, 2011-01-11 22:21
6
5,338 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
7,181 by jruhym
Mon, 2014-04-21 06:47
Normal topic two questions about "Prepare structures for use in Rosetta"
by Anonymous » Wed, 2012-06-06 08:13
6
5,246 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Energy Calculation in Rosetta3.4
by sdg_lab » Thu, 2012-04-12 04:49
6
10,177 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Using Patches in Rosetta
by JS » Wed, 2010-03-10 13:32
6
7,232 by JS
Mon, 2014-04-21 06:47
Normal topic mitochondria protein modeling
by rlwoltz » Fri, 2012-10-26 14:32
6
6,029 by smlewis
Mon, 2014-04-21 06:47
Normal topic ERROR: compiling rosetta3.1 with MPI
by biofisikx » Thu, 2010-08-05 16:00
6
5,729 by smlewis
Mon, 2014-04-21 06:47
Normal topic what rotamer lib is used in rosetta3.5?
by Lindsay » Thu, 2014-02-06 16:11
6
5,412 by rmoretti
Fri, 2014-03-28 09:03
Normal topic Add a ligand with only one atom (i.e. Zn) to the RosettaCM
by lanselibai » Tue, 2021-06-22 10:28
6
1,758 by rmoretti
Thu, 2021-06-24 12:23
Normal topic log files
by shadrinams » Fri, 2018-01-26 07:29
7
5,631 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
5,544 by krdav
Wed, 2016-08-17 12:57
Normal topic about Residue Number in Rosetta
by jiongzhang » Mon, 2012-06-11 14:58
7
9,356 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
9,341 by rmoretti
Mon, 2014-04-21 06:47
Normal topic best_ifaceE.py error
by rosa » Fri, 2013-07-12 08:35
7
5,757 by rosa
Mon, 2014-04-21 06:48
Normal topic A question about Multiple constraints
by kxiao » Mon, 2014-06-16 07:02
7
6,331 by masterofpuppets
Fri, 2014-12-19 08:30
Normal topic Question on eval_atom_derivative function.
by Al52 » Thu, 2015-12-03 16:17
7
5,763 by rmoretti
Thu, 2016-02-04 09:29
Normal topic Using D-amino acids in Rosetta docking
by moehle » Wed, 2011-06-01 00:49
7
7,650 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
6,316 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
5,087 by sunhwan
Mon, 2017-02-27 11:02
Normal topic rerun same experiment on MPI.
by exchhattu » Tue, 2010-02-23 21:14
7
6,161 by exchhattu
Mon, 2014-04-21 06:47
Normal topic How does one prevent Rosetta from connecting two separate chains?
by jhbrown » Thu, 2011-12-15 14:08
7
6,099 by Anonymous
Mon, 2014-04-21 06:47
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57
7
5,658 by smlewis
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
10,648 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
7,058 by Lindsay
Mon, 2014-04-21 06:47
Normal topic relax structure before design?
by Lindsay » Tue, 2013-11-05 20:50
7
8,818 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Error when renumbering PDB
by dzhao » Wed, 2012-07-18 01:03
7
8,362 by rmoretti
Mon, 2014-04-21 06:47
Normal topic hydrophobicity patch
by Lindsay » Fri, 2012-05-04 08:24
7
7,987 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Rosetta (antibody_designer) performance
by Kihang _Youn » Wed, 2022-03-02 00:48
7
1,374 by Kihang _Youn
Thu, 2022-03-10 16:30
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
8,186 by smlewis
Mon, 2014-04-21 06:47
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