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Rosetta 3 - General

Topic / Topic starter Repliessort ascending Views Last post
Normal topic How to generate symmdef file for translational symmetry only?
by pitmand » Thu, 2015-05-14 11:34 		2
 3,231 by pitmand
Tue, 2015-05-26 12:20
Normal topic Clustering Rosetta output PDB files
by ritacc18 » Sat, 2014-01-11 20:13 		2
 5,829 by jwillis
Sat, 2015-06-27 21:11
Normal topic What is "residue packing", "repacking", and so on?
by cossio » Wed, 2014-12-03 08:49 		2
 3,901 by cossio
Wed, 2014-12-03 14:51
Normal topic scoring with omega energy term
by SergeyP » Thu, 2017-03-09 12:03 		2
 2,803 by SergeyP
Fri, 2017-03-10 11:16
Normal topic FARFAR2 Error With Secondary Structure File
by bdh81 » Thu, 2023-11-02 09:01 		2
 620 by bdh81
Sun, 2023-11-05 16:04
Normal topic Running time of Rosetta/FlexPepDock
by gerdos » Thu, 2015-10-15 02:14 		2
 2,837 by gerdos
Fri, 2015-10-16 03:01
Normal topic Rosetta numbering with missing occupancies
by ShaneOConnor » Fri, 2011-10-07 16:18 		2
 3,701 by ShaneOConnor
Mon, 2014-04-21 06:47
Normal topic RASREC - finding lowest energy structure
by Lati » Fri, 2015-11-20 03:08 		2
 2,997 by Lati
Tue, 2016-01-12 13:28
Normal topic DockingProtocol mover ensemble error
by dfcoelho » Tue, 2018-10-16 08:32 		2
 2,738 by brspurri
Thu, 2020-08-20 13:22
Normal topic Rigid Body & Flexible Minimization
by Hanieh » Thu, 2014-02-06 12:37 		2
 4,085 by Hanieh
Fri, 2014-02-28 12:43
Normal topic Error reading new residue .param file
by mgrom92 » Tue, 2016-03-22 12:54 		2
 4,521 by mgrom92
Wed, 2016-03-23 16:45
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32 		2
 1,142 by Ken
Wed, 2022-08-17 08:04
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36 		2
 2,736 by biofisikx
Mon, 2014-04-21 06:47
Normal topic How to prevent rotamers from being pruned from the interaction graph?
by msun » Wed, 2013-04-17 14:19 		2
 2,981 by smlewis
Mon, 2014-04-21 06:47
Normal topic Adding centroid .params files for non-canonical residues based on all-atom .params files
by jcminerlanl » Thu, 2017-04-27 09:28 		2
 2,734 by vmulligan
Thu, 2017-04-27 16:41
Normal topic The concept of unsatisfied hydrogen bond
by asbelx » Wed, 2018-04-25 01:32 		2
 3,396 by asbelx
Thu, 2018-04-26 00:23
Normal topic Controlling Input in the Tutorial
by Smbat » Wed, 2020-07-29 22:41 		2
 1,795 by Smbat
Thu, 2020-07-30 03:07
Normal topic Differences between energy values reported in the tutorials and the ones obtained by running the code, what is normal?
by ericlang » Mon, 2021-07-05 05:43 		2
 1,389 by ericlang
Mon, 2021-07-05 06:59
Normal topic Specifying sidechain NOE restraints in Relax!
by kalabharath » Mon, 2012-12-10 16:44 		2
 3,160 by kalabharath
Mon, 2014-04-21 06:47
Normal topic Using NCAAs in protocols with native heme proteins
by htorres » Wed, 2018-01-24 08:32 		2
 2,872 by htorres
Mon, 2018-02-05 06:53
Normal topic de novo protein prediction
by pci112 » Tue, 2021-03-23 10:13 		2
 1,652 by pci112
Thu, 2021-03-25 01:44
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37 		2
 3,697 by smlewis
Mon, 2014-04-21 06:47
Normal topic Does Rosetta have a separate refinement function?
by ylwang » Tue, 2019-09-24 19:08 		2
 2,103 by ylwang
Tue, 2019-10-08 18:34
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04 		2
 3,806 by smlewis
Mon, 2014-04-21 06:47
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11 		2
 3,264 by Trentage
Mon, 2014-04-21 06:47
Normal topic Patches for post-translational modifications
by ltrabuco » Tue, 2011-02-22 01:00 		2
 4,210 by ltrabuco
Mon, 2014-04-21 06:47
Normal topic Using mode=profile
by Biokhar » Fri, 2012-07-06 00:29 		2
 3,913 by scombs
Mon, 2014-04-21 06:47
Normal topic Is the Fold&Dock protocol availabe in Rosetta3.1
by justin » Mon, 2011-01-17 02:41 		2
 2,607 by smlewis
Mon, 2014-04-21 06:47
Normal topic -RBSegmentRelax:cst_wt not present in ca_to_allatom.linuxgccrelease application?
by Karol » Thu, 2016-05-12 06:30 		2
 2,750 by Karol
Thu, 2016-05-12 07:58
Normal topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:18 		2
 2,289 by jalan
Sun, 2020-04-12 08:01
Normal topic Residue variant types and fragments
by jadolfbr » Mon, 2013-01-21 09:01 		2
 3,368 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic No RMS and IRMS values in protein/nucleic acid docking
by rbeier1 » Wed, 2016-01-13 12:41 		2
 3,453 by smlewis
Thu, 2016-01-14 08:19
Normal topic Error in flex ddG tutorial
by wentlewi » Sat, 2020-05-16 08:06 		2
 2,029 by Alvin Yang
Wed, 2023-10-04 03:34
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57 		2
 2,669 by smlewis
Mon, 2014-04-21 06:47
Normal topic De novo backbone trace from fragments
by Victor Tobiasson » Tue, 2020-12-22 06:34 		2
 2,083 by Victor Tobiasson
Tue, 2020-12-22 09:18
Normal topic ERROR: PDB reader is ignoring atom
by phanvy » Wed, 2014-04-16 17:59 		2
 3,830 by phanvy
Mon, 2014-04-21 03:58
Normal topic which make_fragments.pl
by renedominik » Mon, 2018-06-04 08:58 		2
 3,515 by renedominik
Sat, 2018-07-07 03:03
Normal topic RosettaRemodel gives no increased output when setting higher -num_trajectory
by JW_24 » Tue, 2020-09-22 11:49 		2
 1,746 by JW_24
Wed, 2020-09-23 01:27
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12 		2
 1,437 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic Docking antibody to membrane protein
by Yegor_Ko » Thu, 2023-10-12 07:37 		2
 696 by Yegor_Ko
Fri, 2023-10-20 01:35
Normal topic Error when clustering the output from a docking study
by jos » Thu, 2011-09-08 03:26 		2
 3,515 by jos
Mon, 2014-04-21 06:47
Normal topic Rosetta Resfile header
by G Mustafa » Mon, 2020-01-20 06:45 		2
 2,400 by G Mustafa
Tue, 2020-01-21 06:04
Normal topic score against rmsd plot of designs
by LanMei » Mon, 2022-03-21 22:46 		2
 1,251 by LanMei
Tue, 2022-03-22 20:45
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59 		2
 3,759 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Talaris scoring function
by Lindsay » Sun, 2014-08-24 18:16 		2
 6,518 by AndrewLeaver-Fay
Sun, 2015-09-20 19:34
Normal topic what is the xxx.static.linuxgccrelease?
by syoifczeri » Sat, 2015-10-31 04:09 		2
 6,268 by syoifczeri
Mon, 2015-11-02 03:59
Normal topic ERROR: Not complementary at positions
by szcshr123 » Fri, 2021-02-26 05:58 		2
 2,001 by szcshr123
Fri, 2021-02-26 14:41
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44 		2
 2,667 by ndousis
Mon, 2014-04-21 06:47
Normal topic Modelling Sheets
by monteirotorres » Thu, 2009-07-02 11:41 		2
 2,977 by monteirotorres
Mon, 2014-04-21 06:47
Normal topic runtime error
by exchhattu » Wed, 2010-03-03 02:54 		2
 2,648 by exchhattu
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax with restraints/constraints
by jtmacd » Mon, 2011-07-11 07:07 		2
 4,361 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Calibur not listing cluster members
by Swillard » Sun, 2018-07-01 13:07 		2
 2,501 by benhardy
Fri, 2021-05-07 07:22
Normal topic Constraining a docking study
by jos » Tue, 2011-10-18 05:26 		2
 2,767 by rmoretti
Mon, 2014-04-21 06:47
Normal topic "Local sequence-structure compatability" in "design of ideal protein structures"
by petrikigor » Sun, 2012-12-02 09:25 		2
 3,278 by petrikigor
Mon, 2014-04-21 06:47
Normal topic changing the chain id
by aneamtu » Tue, 2018-01-09 00:08 		2
 4,997 by aneamtu
Thu, 2018-01-18 00:56
Normal topic MPI optimization on TACC stampede2 HPC
by rlwoltz » Tue, 2021-03-16 18:07 		2
 2,186 by rlwoltz
Wed, 2021-03-24 22:36
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06 		2
 3,564 by vanita
Mon, 2014-04-21 06:47
Normal topic rosetta run error
by isengupta13 » Thu, 2010-06-03 19:00 		2
 3,244 by aminzia
Fri, 2019-07-26 13:14
Normal topic ligand docking
by hong wei » Thu, 2021-11-18 05:01 		2
 1,434 by hong wei
Thu, 2021-11-25 02:46
Normal topic Different dG_separated from RAbD and InterfaceAnalyzer
by brubin » Mon, 2022-12-19 13:58 		2
 1,068 by brubin
Tue, 2022-12-20 13:26
Normal topic Using Relax to asses conformational space
by glapidoth11 » Sat, 2011-07-30 05:09 		2
 3,036 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaCM: threading okay, but hybridize loses many secondary structure
by lanselibai » Wed, 2021-06-23 13:51 		2
 1,385 by lanselibai
Thu, 2021-06-24 10:16
Normal topic Creating new residue type for pyridoxal phosphate bound to lysine (LLP) [Solved]
by franfdez » Sat, 2012-01-28 11:39 		1
 3,407 by franfdez
Mon, 2014-04-21 06:47
Normal topic Mutations are ignored (fixbb) when using -auto_setup_metals option
by hdelrisco » Wed, 2019-06-19 15:43 		1
 1,561 by smlewis
Fri, 2019-06-28 13:56
Normal topic Better minimization with Rosetta
by Elijah_Hix » Wed, 2021-07-28 13:53 		1
 1,215 by matteoferla
Mon, 2021-08-09 01:53
Normal topic Scripts and/or strategies for saturation mutagenesis simulations?
by drinker615 » Tue, 2024-04-16 18:43 		1
 200 by rmoretti
Thu, 2024-06-20 13:39
Normal topic Calculate ddG in mutation scan of a homodimer
by zachdebruine » Thu, 2018-02-01 10:02 		1
 1,879 by rmoretti
Mon, 2018-02-05 15:44
Normal topic Relax output mmCIF file to a particular path
by AJVincelli » Sun, 2018-11-25 11:04 		1
 1,649 by AJVincelli
Sun, 2018-11-25 11:09
Normal topic what kind of focefield does Rosetta based on?
by albumns » Tue, 2010-07-06 11:08 		1
 2,224 by smlewis
Mon, 2014-04-21 06:47
Normal topic nbr_atom in ligand docking
by phanvy » Fri, 2015-07-03 07:40 		1
 2,483 by rmoretti
Fri, 2015-07-03 13:04
Normal topic Error in Hybridize of Rosetta Comparative Modeling.
by Ivan » Fri, 2019-11-01 07:46 		1
 1,445 by rmoretti
Mon, 2019-11-04 12:54
Normal topic constraint are not imposed during protein-ligand docking
by rohi » Wed, 2020-12-02 11:28 		1
 1,508 by rmoretti
Tue, 2021-02-09 12:02
Normal topic Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.
by SubhaK » Thu, 2023-01-26 21:29 		1
 706 by rmoretti
Mon, 2023-02-06 14:35
Normal topic problems in building rosetta3.1 (solved)
by zpliu09 » Wed, 2010-03-31 02:03 		1
 2,075 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input pdb to rosetta format add "missing" residues to pdb file
by zhisheng » Tue, 2011-06-07 09:51 		1
 3,996 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problems with parametrisation
by DmitriiN » Fri, 2016-05-27 04:51 		1
 2,235 by rmoretti
Tue, 2016-07-12 08:43
Normal topic Unable to create col_complex.pdb file
by sayan500 » Tue, 2019-07-30 22:08 		1
 1,502 by rmoretti
Mon, 2019-08-26 14:52
Normal topic the question about ddg of disulfide bond mutants
by asbelx » Sun, 2021-08-29 06:40 		1
 1,209 by asbelx
Wed, 2021-09-08 23:19
Normal topic Question about blueprint file generation
by ng98 » Fri, 2024-05-24 03:02 		1
 92 by rmoretti
Thu, 2024-06-20 13:25
Normal topic How to create a rotamer set that includes all possible rotamers of all possible amino acids
by AyushGoyal » Thu, 2014-11-06 10:37 		1
 2,536 by smlewis
Fri, 2014-11-07 12:03
Normal topic Protein Interface Design using PSSM
by ccruz » Sun, 2020-05-24 14:27 		1
 2,098 by nannemdp
Tue, 2020-05-26 06:33
Normal topic PDB output sum
by enoee » Fri, 2010-07-16 12:29 		1
 2,226 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta/PyRosetta on GPU
by ac.research » Mon, 2017-11-06 05:18 		1
 5,150 by rmoretti
Mon, 2017-11-06 07:36
Normal topic ab initio struction prediction
by Negarsardar » Mon, 2018-08-06 15:50 		1
 1,712 by smlewis
Tue, 2018-08-07 16:59
Normal topic clustering ligand binding mood by ligand RMSD
by rohi » Tue, 2021-01-26 21:11 		1
 1,583 by brownbp1
Tue, 2021-02-09 12:12
Normal topic Installing rosetta 3.0
by dalemu » Thu, 2009-09-24 13:28 		1
 2,913 by smlewis
Mon, 2014-04-21 06:47
Normal topic 3D Structure Prediction
by anirbanzz » Sat, 2010-04-17 02:47 		1
 2,786 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to run docking in rosetta with small molecule
by ajaniharesh » Tue, 2012-02-28 03:58 		1
 4,012 by smlewis
Mon, 2014-04-21 06:47
Normal topic Binary silent Output file reading problem
by wlzhang » Sun, 2014-04-20 17:47 		1
 2,475 by wlzhang
Sun, 2014-04-20 18:17
Normal topic pKa prediction using the Rosetta scoring function
by das » Tue, 2016-06-21 06:42 		1
 2,014 by ssrb
Tue, 2016-07-12 10:02
Normal topic Score function: unable to open input_files/1qys.pdb
by Cyrrusm » Tue, 2020-10-13 11:35 		1
 1,493 by rmoretti
Tue, 2020-10-13 11:40
Normal topic start pose and native pose don't match in lengh
by zhisheng » Thu, 2011-12-15 10:23 		1
 2,498 by smlewis
Mon, 2014-04-21 06:47
Normal topic run:test_cycles
by ramin » Sun, 2013-03-10 11:05 		1
 2,195 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33 		1
 3,581 by rmoretti
Wed, 2014-12-03 18:52
Normal topic Rosetta matching error
by purvi24 » Mon, 2018-03-12 02:38 		1
 2,314 by smlewis
Mon, 2018-03-12 09:57
Normal topic Rosetta params for taxol
by ahmadkhalifa » Sat, 2019-03-30 22:37 		1
 1,586 by rmoretti
Wed, 2019-04-03 10:03
Normal topic error when using script best_ifaceE.py
by windmill » Thu, 2020-06-18 21:30 		1
 1,327 by windmill
Thu, 2020-06-18 21:32
Normal topic ab initio protein structure prediction
by croshong » Wed, 2009-12-16 23:25 		1
 2,315 by smlewis
Mon, 2014-04-21 06:47
Normal topic Question about wrong homology design
by mony2182 » Fri, 2014-07-04 10:26 		1
 2,448 by rmoretti
Mon, 2014-07-07 08:08
Normal topic Negative fa_rep on ddG ?
by LiorZ » Thu, 2016-09-08 07:44 		1
 1,929 by rmoretti
Thu, 2016-09-08 07:56