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Rosetta 3 - General

Topic / Topic starter Repliessort descending Views Last post
Normal topic Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41 		4
 4,544 by linucks
Fri, 2018-02-23 08:08
Normal topic Fragment files
by exchhattu » Fri, 2009-09-18 01:04 		4
 4,826 by rmoretti
Tue, 2015-01-06 09:58
Normal topic Ab initio structure prediction for long amino acid sequence
by maruhuang » Fri, 2019-08-02 03:38 		4
 3,237 by maruhuang
Thu, 2019-09-26 18:55
Normal topic Enzyme Design
by bharat_46010 » Tue, 2014-11-25 23:55 		4
 6,296 by bharat_46010
Mon, 2014-12-15 20:51
Normal topic The vall.jul19.2011.gz Database
by ac.research » Fri, 2017-09-01 02:29 		4
 4,719 by ac.research
Mon, 2017-09-04 16:43
Normal topic Does a negative Rosetta dG imply a favorable process?
by cossio » Tue, 2014-12-09 05:13 		4
 4,981 by lanselibai
Tue, 2014-12-16 10:48
Normal topic membrane protein packing prediction
by djpittdj » Fri, 2012-01-13 08:55 		4
 4,339 by pardave
Mon, 2014-04-21 06:47
Normal topic How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches
by zaldini » Fri, 2015-01-02 05:53 		4
 4,764 by zaldini
Wed, 2015-01-07 20:35
Normal topic Relax protocoll short pdb of AAA petide
by knutjbj » Wed, 2011-01-26 05:01 		5
 5,184 by smlewis
Mon, 2014-04-21 06:47
Normal topic About align hundreds of pdb structures produced by rosseta membrane abinitio
by ritacc18 » Wed, 2013-05-22 12:37 		5
 6,893 by ssrb
Tue, 2015-09-22 08:35
Normal topic RosettaDock decoys recoring with ZRANK
by cheyuk » Fri, 2014-04-11 01:40 		5
 8,225 by rmoretti
Thu, 2016-04-28 15:53
Normal topic De novo Protein Design
by ac.research » Sat, 2017-07-15 10:39 		5
 8,894 by rmoretti
Mon, 2017-08-14 09:06
Normal topic Reading FE from 2PAH
by jadolfbr » Tue, 2013-01-29 16:10 		5
 6,613 by rmoretti
Mon, 2014-04-21 06:47
Normal topic extraction of pdbs from silent.out files on Mac
by pramod » Tue, 2014-01-07 11:43 		5
 7,580 by rmoretti
Mon, 2014-04-21 06:48
Normal topic combine_silent ERROR: unknown atom_name: CYS SG
by freedman » Mon, 2017-03-06 10:56 		5
 4,547 by freedman
Mon, 2017-03-06 13:24
Normal topic Question regarding buried or exposed residues
by qlj » Fri, 2012-11-09 23:43 		5
 6,747 by qlj
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 cluster pdb structures questions
by ritacc18 » Thu, 2013-03-28 19:20 		5
 7,298 by ritacc18
Mon, 2014-04-21 06:47
Normal topic Computing energy gradients for side chain minimization
by pachecoj » Wed, 2017-03-29 08:03 		5
 4,900 by pachecoj
Wed, 2017-03-29 12:32
Normal topic low resolution blind protein-protein docking with a ligand
by einew » Sun, 2011-03-20 13:59 		5
 6,112 by einew
Mon, 2014-04-21 06:47
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 Docking tree issues
by salvatta » Tue, 2018-07-17 05:57 		5
 5,356 by salvatta
Mon, 2018-09-10 10:04
Normal topic how to use AbinitioRelax.mpi.linuxgccrelease?
by albumns » Mon, 2012-03-26 22:50 		5
 6,866 by smlewis
Mon, 2014-04-21 06:47
Normal topic Issues with rosetta numbering and keeping ligand when relaxing molecule.
by Wexter300 » Sun, 2024-04-28 14:37 		5
 545 by rmoretti
Thu, 2024-06-20 13:28
Normal topic Error when using RabD with a nanobody.
by zhangying1990 » Mon, 2018-12-17 04:40 		5
 4,308 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
 5,355 by rpache
Mon, 2014-04-21 06:47
Normal topic de novo RNA loop
by c.ocasion » Sun, 2021-02-14 18:34 		5
 2,988 by everyday847
Mon, 2021-03-29 20:19
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 Chain specific flags
by helenah » Mon, 2020-10-19 03:31 		5
 3,260 by rmoretti
Fri, 2020-11-06 08:04
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 rosetta_scripts_BOGUS coords warning message
by Karol » Tue, 2016-12-13 02:35 		5
 5,800 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
 2,320 by matteoferla
Fri, 2022-07-01 13:49
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 Rotate MOVER
by gw » Wed, 2012-08-15 12:09 		5
 5,478 by glemmon
Mon, 2014-04-21 06:47
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 Error when running "plot_LHOC.py"
by Sunyp_IM » Sun, 2017-08-13 05:54 		5
 4,538 by smlewis
Wed, 2017-08-16 08:30
Normal topic match_dspos1 and other matcher options
by petrikigor » Sat, 2012-10-20 09:22 		5
 5,775 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
 4,636 by Loki01
Thu, 2017-12-14 06:20
Normal topic P-P docking with ambiguous constraints
by Anouk » Fri, 2013-11-08 11:38 		5
 6,899 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Rotamer Library Generation in Rosetta3
by jcminerlanl » Wed, 2016-11-30 07:34 		5
 6,242 by rmoretti
Tue, 2021-02-09 11:52
Normal topic Interface rmsd calculation Irms
by mahajanr » Wed, 2010-07-07 18:24 		5
 8,063 by mahajanr
Mon, 2014-04-21 06:47
Normal topic BridgeChainsMover
by msardejani » Sun, 2016-08-07 17:32 		5
 5,238 by smlewis
Tue, 2016-08-30 13:47
Normal topic Relax command for docking purposes and cluster_vs_rmsd command
by Rkfoury » Wed, 2015-04-01 08:48 		5
 5,885 by rmoretti
Sat, 2015-04-25 10:05
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33 		5
 5,436 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
 5,048 by rmoretti
Thu, 2017-08-03 09:01
Normal topic Rosetta-foldtree and docking
by tingting » Tue, 2022-03-15 22:49 		5
 2,439 by aastha.pal
Mon, 2022-06-27 09:55
Normal topic Evaluating energies on non-standard rotamer set
by pachecoj » Sat, 2014-07-26 16:27 		5
 5,181 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
 4,774 by smlewis
Tue, 2018-07-03 11:22
Normal topic Secondary Structure Relax
by ac.research » Sat, 2018-03-17 10:50 		5
 4,998 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
 6,830 by einew
Mon, 2014-04-21 06:47
Normal topic Suppress printing to STDOUT for applications
by tylerborrman » Tue, 2015-11-24 11:37 		5
 5,837 by code_Monkey
Thu, 2021-03-18 08:03
Normal topic P(Res | phi,psi )
by jadolfbr » Thu, 2011-07-21 08:49 		5
 5,063 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic RosettaMatch
by jtmacd » Wed, 2012-01-11 06:50 		5
 10,416 by jtmacd
Mon, 2014-04-21 06:47
Normal topic industrial example of ROSETTA modeled protein
by banshee » Sat, 2016-04-23 23:40 		5
 5,410 by banshee
Tue, 2016-04-26 00:47
Normal topic Problem with relaxing a PDB around a chemically bound ligand
by drinker615 » Sat, 2024-04-06 16:04 		5
 621 by drinker615
Tue, 2024-04-16 19:06
Normal topic How to extract specific pdb from silent files
by eunwook » Tue, 2013-05-14 05:29 		5
 16,010 by nawsad
Mon, 2014-04-21 06:47
Normal topic nr.fasta
by silvia » Wed, 2013-01-23 10:08 		5
 10,800 by dgront
Mon, 2014-04-21 06:47
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 Modeling only part of the protein structure using ROSETTA
by qiongwu » Fri, 2009-05-29 09:08 		5
 5,123 by smlewis
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
 5,721 by rmoretti
Tue, 2015-05-05 14:31
Normal topic Cannot use SimpleMetrics
by Vedasheersh » Sun, 2018-06-10 23:38 		5
 4,159 by smlewis
Tue, 2018-06-12 10:54
Normal topic demos/public/ideal_proteins Segmentation fault
by coomteng@gmail.com » Wed, 2018-03-07 00:15 		5
 4,279 by rmoretti
Thu, 2018-03-08 07:46
Normal topic Error running snugdock
by SenyorDrew » Tue, 2017-03-14 10:00 		5
 5,019 by SenyorDrew
Wed, 2017-03-29 06:40
Normal topic Rosetta repacking output
by doranhen » Mon, 2012-12-03 03:44 		5
 6,135 by doranhen
Mon, 2014-04-21 06:47
Normal topic Robetta fragments and silent.out-file
by masterofpuppets » Wed, 2015-01-07 04:28 		5
 6,634 by masterofpuppets
Tue, 2015-02-10 03:15
Normal topic Docking double-stranded DNA to a protein
by xpzhang » Tue, 2012-01-31 12:35 		5
 9,042 by xpzhang
Mon, 2014-04-21 06:47
Normal topic Is cis-Glycine okay?
by matteoferla » Tue, 2019-11-19 07:26 		5
 3,893 by matteoferla
Wed, 2019-11-20 02:32
Normal topic Unrecognized residue Glc
by cgautier » Tue, 2015-03-31 02:20 		5
 6,617 by rmoretti
Thu, 2015-04-16 10:09
Normal topic Encouraging better packing in enzyme_design
by linucks » Thu, 2018-03-01 07:05 		5
 6,071 by linucks
Wed, 2018-04-25 08:50
Normal topic ClusterApp hogs way too much memory...
by IgaK » Tue, 2009-09-29 00:14 		5
 5,173 by w107kdk
Mon, 2014-04-21 06:47
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 Produces a set of rotamers from a given residue
by a-eatemadi@razi... » Tue, 2017-08-15 08:05 		5
 5,616 by a-eatemadi@razi...
Fri, 2017-09-15 07:45
Normal topic defining interface in interface analyzer
by aa20 » Fri, 2013-09-27 11:08 		5
 7,221 by smlewis
Mon, 2014-04-21 06:48
Normal topic segmentation fault when using design_hpatch scoring function
by rbjacob » Mon, 2018-04-09 11:05 		5
 4,088 by smlewis
Wed, 2018-04-11 11:45
Normal topic dun10
by jadolfbr » Thu, 2012-01-19 12:16 		5
 5,296 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Scoring Electrostatics
by aroop » Tue, 2012-08-07 11:41 		5
 5,799 by aroop
Mon, 2014-04-21 06:47
Normal topic modeling residues with covalent ligand attachments
by sid » Fri, 2011-04-15 09:16 		5
 8,103 by rmoretti
Fri, 2015-07-03 14:02
Normal topic Rosetta Antibody Prepack - Problem HL_A vs. LH_A
by cannond » Fri, 2017-03-03 02:41 		5
 5,683 by cannond
Wed, 2017-03-08 03:00
Normal topic Make_fragments.pl database
by TiagoGomes » Tue, 2009-10-13 11:31 		5
 4,933 by matteoferla
Wed, 2021-09-29 01:58
Normal topic questions about ab init membrane protein
by albumns » Mon, 2011-02-07 01:09 		5
 5,540 by zeynep
Mon, 2014-04-21 06:47
Normal topic calculate RMSD (RNA modelling)
by obdulia » Tue, 2016-07-05 01:58 		5
 6,339 by obdulia
Wed, 2016-07-13 09:11
Normal topic Loop modeling with ligand in the receptor
by cno » Mon, 2010-12-13 14:07 		5
 6,603 by smlewis
Mon, 2014-04-21 06:47
Normal topic protocols.jd2.JobDistributor: [ ERROR ]
by johnnytam100 » Thu, 2019-04-11 09:30 		5
 5,051 by jadolfbr
Tue, 2019-04-16 09:15
Normal topic ab inito memberane error
by albumns » Mon, 2011-02-14 10:58 		5
 8,288 by albumns
Mon, 2014-04-21 06:47
Normal topic uninstalling or rebuilding rosetta
by rlwoltz » Thu, 2013-04-11 11:45 		5
 8,052 by rlwoltz
Mon, 2014-04-21 06:47
Normal topic setting timeout option in MPI run
by syntekabio2019 » Mon, 2024-02-26 01:09 		5
 799 by rmoretti
Wed, 2024-02-28 09:20
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30 		6
 14,002 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
 7,736 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
 7,813 by tigerous
Mon, 2014-04-21 06:47
Normal topic Cannot run binaries after successful compilation
by ac.research » Mon, 2017-08-14 02:56 		6
 7,562 by ac.research
Fri, 2017-08-18 00:57
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 NR Database Download in install_dependencies.pl (for make_fragments.pl) Broken
by Jacob_Verburgt » Tue, 2020-03-10 08:58 		6
 5,742 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
 6,447 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
 1,971 by rmoretti
Mon, 2023-02-20 16:07
Normal topic distances definition in course-grained (centroid mode) steps
by allan.ferrari » Tue, 2017-01-03 05:15 		6
 5,582 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
 4,494 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
 7,377 by smlewis
Mon, 2014-04-21 06:47
Normal topic Linker problems when building mini
by assaff » Mon, 2009-10-12 01:07 		6
 5,843 by smlewis
Mon, 2014-04-21 06:47
Normal topic SASA packing score in Rosetta 3.1
by enoee » Wed, 2010-07-28 01:45 		6
 6,996 by smlewis
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
 5,160 by albumns
Mon, 2014-04-21 06:47