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Rosetta 3 - General

Topic / Topic starter Replies Viewssort ascending Last post
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 How the Rosetta score (dG) is actually related to dH (enthalpy) and dS (entropy)?
by lanselibai » Thu, 2014-12-04 13:16 		4
 6,553 by lanselibai
Fri, 2014-12-12 10:27
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40 		7
 6,549 by rmoretti
Mon, 2014-04-21 06:47
Normal topic total energy score of the pdb structure
by Lindsay » Tue, 2012-05-01 12:14 		4
 6,549 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Comparative Modeling databases?
by nitroamos » Wed, 2011-11-23 14:54 		6
 6,548 by rmoretti
Thu, 2016-04-28 16:15
Normal topic Talaris scoring function
by Lindsay » Sun, 2014-08-24 18:16 		2
 6,516 by AndrewLeaver-Fay
Sun, 2015-09-20 19:34
Normal topic CryoEM model refinement with covalent conjugated prosthetic Phosphopantetheine carrying acyl group
by ZhijunW » Thu, 2020-09-03 18:36 		11
 6,504 by matteoferla
Sat, 2020-09-12 03:02
Normal topic '-norepack_disulf' flag NOT work in Ligand-protein docking ?
by darlintai » Tue, 2011-01-11 22:21 		6
 6,465 by smlewis
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
 6,444 by brandon.frenz
Tue, 2018-03-20 10:28
Normal topic dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.
by jyotisutar9 » Thu, 2016-12-01 00:39 		6
 6,441 by jyotisutar9
Wed, 2016-12-14 09:39
Normal topic Interface energy vs binding energy
by Apiwat » Wed, 2014-02-05 00:47 		2
 6,434 by Apiwat
Sat, 2014-02-08 01:41
Normal topic computer specifications
by rlwoltz » Tue, 2012-10-09 16:11 		4
 6,429 by rlwoltz
Mon, 2014-04-21 06:47
Normal topic Problem With Rosetta3.3 Comparative/Loop Modeling And Constraints
by jurkm » Mon, 2011-09-12 01:01 		6
 6,400 by jurkm
Mon, 2014-04-21 06:47
Normal topic RosettaHoles
by ge0rgekh0ury » Mon, 2012-01-09 09:01 		6
 6,395 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
 6,369 by robren
Mon, 2014-04-21 06:47
Normal topic What's the unit of Rosetta energy function?
by Run » Tue, 2014-06-24 00:44 		1
 6,349 by rmoretti
Tue, 2014-07-01 12:45
Normal topic Antibody homology modeling fails after blastp
by sunhwan » Sat, 2017-02-18 11:25 		7
 6,335 by sunhwan
Mon, 2017-02-27 11:02
Normal topic calculate RMSD (RNA modelling)
by obdulia » Tue, 2016-07-05 01:58 		5
 6,334 by obdulia
Wed, 2016-07-13 09:11
Normal topic Enzyme Design
by bharat_46010 » Tue, 2014-11-25 23:55 		4
 6,292 by bharat_46010
Mon, 2014-12-15 20:51
Normal topic force field, energy function
by masterofpuppets » Wed, 2015-01-21 11:06 		3
 6,287 by masterofpuppets
Tue, 2015-01-27 07:07
Normal topic membrane ab initio error after montecarlo
by adva » Mon, 2012-12-24 01:43 		6
 6,284 by tevang
Mon, 2014-04-21 06:47
Normal topic calculated ddG_bind converges to zero
by fukamitka » Mon, 2013-06-24 20:32 		6
 6,272 by fukamitka
Mon, 2014-04-21 06:48
Normal topic what is the xxx.static.linuxgccrelease?
by syoifczeri » Sat, 2015-10-31 04:09 		2
 6,266 by syoifczeri
Mon, 2015-11-02 03:59
Normal topic pro_closure energy scoring function
by peony » Sat, 2013-11-16 13:22 		5
 6,265 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Problems installing Rosetta
by S » Fri, 2010-09-03 01:04 		4
 6,247 by abdullah_ahmed
Mon, 2014-04-21 06:47
Normal topic Rotamer Library Generation in Rosetta3
by jcminerlanl » Wed, 2016-11-30 07:34 		5
 6,237 by rmoretti
Tue, 2021-02-09 11:52
Normal topic two questions about "Prepare structures for use in Rosetta"
by Anonymous » Wed, 2012-06-06 08:13 		6
 6,237 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Can anyone become a Rosetta developer?
by cossio » Thu, 2015-01-22 05:10 		4
 6,204 by cossio
Thu, 2015-01-29 11:50
Normal topic Abinitio Calculations - typical parameters
by vamsi » Thu, 2010-11-11 07:06 		5
 6,167 by smlewis
Mon, 2014-04-21 06:47
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 Fixed bb design with hydrogen bond constraint
by bharat_46010 » Mon, 2012-04-30 22:56 		6
 6,148 by smlewis
Mon, 2014-04-21 06:47
Normal topic What is "repack", "prepack"?
by cossio » Wed, 2015-11-04 17:59 		1
 6,134 by rmoretti
Tue, 2015-11-10 11:52
Normal topic Rosetta repacking output
by doranhen » Mon, 2012-12-03 03:44 		5
 6,134 by doranhen
Mon, 2014-04-21 06:47
Normal topic low resolution blind protein-protein docking with a ligand
by einew » Sun, 2011-03-20 13:59 		5
 6,111 by einew
Mon, 2014-04-21 06:47
Normal topic modeling loops between domains
by dhorita » Thu, 2009-03-05 14:48 		6
 6,109 by jarod
Mon, 2014-04-21 06:47
Normal topic rosetta 3.1-how to run parallel tasks?
by wtscrystal » Fri, 2009-11-06 03:23 		4
 6,098 by lqzhang
Mon, 2014-04-21 06:47
Normal topic loop modelling/Rosetta 3.4, 3.5
by berk » Tue, 2013-07-02 08:38 		5
 6,091 by MRH
Mon, 2014-04-21 06:48
Normal topic Rosetta job distribution error
by ss » Thu, 2019-08-01 09:26 		8
 6,083 by ac.research
Mon, 2020-02-10 08:19
Normal topic protein binding energy problem
by Lindsay » Thu, 2014-04-17 23:10 		5
 6,072 by jadolfbr
Mon, 2014-04-21 07:30
Normal topic scoring models
by peony » Fri, 2013-12-06 02:45 		5
 6,069 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Encouraging better packing in enzyme_design
by linucks » Thu, 2018-03-01 07:05 		5
 6,066 by linucks
Wed, 2018-04-25 08:50
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 protein protein docking pipeline
by dzhao » Thu, 2012-07-19 06:25 		4
 6,058 by smlewis
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
 5,965 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Problem with HETATM entries in PDB file
by asmi » Fri, 2011-05-20 10:17 		3
 5,950 by smlewis
Mon, 2014-04-21 06:47
Normal topic Connecting 2 Domains Via Non-Flexible Linker
by jurkm » Mon, 2011-09-05 06:10 		2
 5,948 by kbuhr
Tue, 2015-07-14 04:30
Normal topic Membrane folding - blastpgp error.
by arthuc01 » Sun, 2012-03-25 14:47 		4
 5,948 by arthuc01
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
 5,895 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Relax command for docking purposes and cluster_vs_rmsd command
by Rkfoury » Wed, 2015-04-01 08:48 		5
 5,880 by rmoretti
Sat, 2015-04-25 10:05
Normal topic Linker problems when building mini
by assaff » Mon, 2009-10-12 01:07 		6
 5,843 by smlewis
Mon, 2014-04-21 06:47
Normal topic Suppress printing to STDOUT for applications
by tylerborrman » Tue, 2015-11-24 11:37 		5
 5,832 by code_Monkey
Thu, 2021-03-18 08:03
Normal topic abinitiorelax: No funnel
by cno » Tue, 2010-07-27 06:14 		6
 5,831 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Clustering Rosetta output PDB files
by ritacc18 » Sat, 2014-01-11 20:13 		2
 5,827 by jwillis
Sat, 2015-06-27 21:11
Normal topic Error : seqpos <= size()
by phanvy » Sun, 2014-10-05 17:20 		4
 5,813 by phanvy
Wed, 2014-10-08 01:42
Normal topic Missing atoms, unable to fill in missing atoms
by kwu030 » Fri, 2023-05-05 12:58 		12
 5,805 by kwu030
Thu, 2023-05-18 08:31
Normal topic Scoring Electrostatics
by aroop » Tue, 2012-08-07 11:41 		5
 5,798 by aroop
Mon, 2014-04-21 06:47
Normal topic rosetta_scripts_BOGUS coords warning message
by Karol » Tue, 2016-12-13 02:35 		5
 5,795 by Karol
Thu, 2016-12-15 01:35
Normal topic How to get the GDT_TS?
by JadAbbass » Thu, 2013-09-05 11:59 		3
 5,779 by rmoretti
Mon, 2014-04-21 06:48
Normal topic match_dspos1 and other matcher options
by petrikigor » Sat, 2012-10-20 09:22 		5
 5,774 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Picking the correct model from a large set of decoys (30,000+)
by brspurri » Thu, 2012-04-26 15:37 		4
 5,774 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Questions about Monte Carlo Simulated Annealing algorithm in the design protocols
by mdyini » Thu, 2012-05-31 12:39 		3
 5,765 by smlewis
Mon, 2014-04-21 06:47
Normal topic Public subversion / Enzyme design public app
by weallen » Tue, 2009-08-11 20:50 		6
 5,753 by weallen
Mon, 2014-04-21 06:47
Normal topic Rosetta3.2 cluster application file-reading error
by mdyini » Wed, 2011-03-09 16:59 		3
 5,739 by smlewis
Mon, 2014-04-21 06:47
Normal topic comparison of energy
by sdh » Mon, 2010-08-16 07:55 		5
 5,737 by smlewis
Mon, 2014-04-21 06:47
Normal topic NR Database Download in install_dependencies.pl (for make_fragments.pl) Broken
by Jacob_Verburgt » Tue, 2020-03-10 08:58 		6
 5,736 by Jacob_Verburgt
Wed, 2020-03-11 05:18
Normal topic Native gives higher (positive) than lowest energy and clustered decoys
by tiagogomes89 » Thu, 2011-06-02 07:19 		6
 5,717 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Minimization Issue: Coarse Graining to All atom modeling
by abolia » Tue, 2015-04-28 10:52 		5
 5,716 by rmoretti
Tue, 2015-05-05 14:31
Normal topic a question about loop refinement
by albumns » Fri, 2012-03-02 09:38 		4
 5,700 by albumns
Mon, 2014-04-21 06:47
Normal topic Access sigma values for rotamers
by pachecoj » Thu, 2014-05-15 07:10 		5
 5,697 by rmoretti
Sat, 2014-05-17 14:10
Normal topic Rosetta Antibody Prepack - Problem HL_A vs. LH_A
by cannond » Fri, 2017-03-03 02:41 		5
 5,678 by cannond
Wed, 2017-03-08 03:00
Normal topic MPI nodes hanging and output log incomplete
by yuvals » Wed, 2014-06-18 05:40 		1
 5,669 by yuvals
Sat, 2014-06-21 02:17
Normal topic Can i start again the job ?
by byin » Thu, 2011-09-15 01:19 		6
 5,636 by byin
Mon, 2014-04-21 06:47
Normal topic Produces a set of rotamers from a given residue
by a-eatemadi@razi... » Tue, 2017-08-15 08:05 		5
 5,611 by a-eatemadi@razi...
Fri, 2017-09-15 07:45
Normal topic How to install Rosetta in Redhat Linux ?
by ajaniharesh » Fri, 2012-02-24 02:32 		1
 5,607 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to model a protein that dimerizes to a small molecule?
by pholland » Wed, 2011-05-25 07:29 		3
 5,607 by pholland
Mon, 2014-04-21 06:47
Normal topic Does Rosetta recognise OXT atom type in PDB.?
by monos_morpheus » Mon, 2011-04-11 23:57 		4
 5,595 by monos_morpheus
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
 5,576 by allan.ferrari
Tue, 2017-01-03 11:15
Normal topic rosetta 3.1 recognizes PO4 group in dockinglocalrefine option?
by nilkoeg » Thu, 2011-03-10 23:19 		4
 5,574 by nilkoeg
Mon, 2014-04-21 06:47
Normal topic Ligand conformations file in docking
by rosa » Fri, 2013-07-12 09:21 		4
 5,545 by rosa
Mon, 2014-04-21 06:48
Normal topic questions about ab init membrane protein
by albumns » Mon, 2011-02-07 01:09 		5
 5,539 by zeynep
Mon, 2014-04-21 06:47
Normal topic Discarding atoms for fixbb
by Jacob-kong » Tue, 2012-06-26 06:23 		4
 5,537 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic Problems with Cterm_amidation.txt
by helenah » Thu, 2020-10-08 04:52 		8
 5,511 by helenah
Tue, 2020-11-03 04:33
Normal topic Resfile for fixed backbone design
by dyq » Wed, 2009-10-07 10:50 		5
 5,505 by attesor
Mon, 2014-04-21 06:47
Normal topic Rotate MOVER
by gw » Wed, 2012-08-15 12:09 		5
 5,477 by glemmon
Mon, 2014-04-21 06:47
Normal topic prepare PDB with constrained relax
by jarod » Sun, 2013-05-05 07:10 		3
 5,460 by rmoretti
Mon, 2014-04-21 06:47
Normal topic I have a .tab file. How do I extract information from it?
by monos_morpheus » Tue, 2011-02-08 09:30 		4
 5,457 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic is it possbile to cluster pdb files?
by albumns » Wed, 2010-10-06 02:38 		3
 5,453 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta CM incorrect threading
by ahmadkhalifa » Mon, 2018-08-06 11:09 		6
 5,442 by rmoretti
Fri, 2018-08-24 11:59
Normal topic smoothly kill a mpirun process
by fred » Tue, 2014-02-18 06:06 		2
 5,441 by Ashafix
Wed, 2014-02-19 06:53
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33 		5
 5,431 by rmoretti
Tue, 2014-11-18 10:01
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 industrial example of ROSETTA modeled protein
by banshee » Sat, 2016-04-23 23:40 		5
 5,405 by banshee
Tue, 2016-04-26 00:47
Normal topic loop modelling error on Rosetta3.2 or Rosetta3.3
by exchhattu » Thu, 2011-09-29 03:58 		5
 5,355 by rpache
Mon, 2014-04-21 06:47
Normal topic Docking tree issues
by salvatta » Tue, 2018-07-17 05:57 		5
 5,351 by salvatta
Mon, 2018-09-10 10:04
Normal topic does rosetta good at peptide-protein docking?
by albumns » Mon, 2010-12-27 18:51 		3
 5,338 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 dun10
by jadolfbr » Thu, 2012-01-19 12:16 		5
 5,295 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Suppressing Rosetta output, flag for that?
by msellers » Tue, 2011-04-26 11:18 		4
 5,293 by smlewis
Mon, 2014-04-21 06:47
Normal topic Citing Rosetta3.0
by ctaylor » Fri, 2009-10-09 11:42 		1
 5,273 by smlewis
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18 		2
 5,236 by pepfolder
Mon, 2014-04-21 06:47