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Rosetta 3 - Applications

Topic / Topic starter Replies Viewssort descending Last post
Normal topic Rosetta 3.4 "Relax pdb with allatom constraints" does not work with structures containing multiple chains
by ahonegger » Tue, 2012-04-24 01:34 		3
 4,321 by ahonegger
Mon, 2014-04-21 06:47
Normal topic side chain repacking error
by malkeet.singh » Thu, 2017-12-07 04:49 		4
 4,331 by smlewis
Wed, 2017-12-13 09:54
Normal topic unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file
by Sajjad » Wed, 2022-11-30 11:40 		1
 4,333 by FJOM
Wed, 2023-05-03 07:21
Normal topic RMSD calculation
by hamedkhakzad » Tue, 2016-09-13 04:56 		2
 4,335 by rmoretti
Wed, 2016-09-14 02:05
Normal topic How to run simulations with non-canonical amino acids?
by Denise » Thu, 2017-06-08 07:50 		4
 4,340 by Denise
Thu, 2017-06-15 04:26
Normal topic Constraints in RosettaCM
by kbuhr » Fri, 2015-07-31 06:55 		3
 4,341 by kbuhr
Mon, 2016-03-28 01:08
Normal topic revert_design_to_native app comparison to FavorNativeResidue mover
by nwhoppe » Wed, 2016-06-29 14:35 		3
 4,349 by rmoretti
Tue, 2016-07-12 09:30
Normal topic loopmodel thinks there are no residues in the pose
by lah435 » Wed, 2013-03-27 02:46 		3
 4,350 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Per residue scoring
by chelsell » Mon, 2015-08-17 14:43 		3
 4,359 by rmoretti
Wed, 2015-09-02 12:33
Normal topic partial ab initio modeling
by fred » Wed, 2011-08-17 14:14 		3
 4,362 by smlewis
Mon, 2014-04-21 06:47
Normal topic HBNet and RosettaScripts
by protos_heis » Tue, 2014-08-05 06:05 		3
 4,379 by protos_heis
Tue, 2014-08-05 12:47
Normal topic "sparks failed" error when running "make_fragments.pl"?
by Danielsebas » Tue, 2019-09-03 03:43 		6
 4,384 by Jacob_Verburgt
Tue, 2020-03-10 14:39
Normal topic Multistate design output
by tong » Wed, 2018-06-20 00:21 		6
 4,385 by tong
Sun, 2018-06-24 23:30
Normal topic ddg_monomer.mpi
by gw » Thu, 2011-10-27 16:45 		3
 4,395 by smlewis
Mon, 2014-04-21 06:47
Normal topic membrane ab initio modeling application with constraints
by ytao » Thu, 2012-11-08 11:56 		2
 4,396 by ytao
Mon, 2014-04-21 06:47
Normal topic Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking
by Corvin » Wed, 2019-06-19 08:40 		5
 4,401 by rmoretti
Tue, 2019-07-09 10:13
Normal topic rosetta3.4 fragment file problem
by David Hoover » Wed, 2012-05-16 14:42 		4
 4,408 by dgront
Mon, 2014-04-21 06:47
Normal topic null mutation with ddg_monomer
by fred » Fri, 2012-05-11 07:16 		4
 4,412 by fred
Mon, 2014-04-21 06:47
Normal topic auto_setup_metals flag with loop modeling application fails
by beowulfey » Wed, 2015-06-10 07:44 		3
 4,429 by beowulfey
Tue, 2015-06-23 16:10
Normal topic Changing scoring function for fixbb protocol
by mdyini » Sat, 2012-07-07 18:43 		4
 4,440 by mdyini
Mon, 2014-04-21 06:47
Normal topic RosettaScripts LinkResidues
by Yero » Fri, 2019-05-17 05:26 		5
 4,440 by Yero
Thu, 2019-07-18 01:39
Normal topic Some wrong with the flag "-l" for score_jd2.linuxgccrelease
by lanselibai » Mon, 2014-09-29 02:29 		2
 4,447 by lanselibai
Tue, 2014-09-30 02:28
Normal topic Loop prediction
by yzhou » Thu, 2013-07-18 14:24 		3
 4,457 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic How to minimize the decoys obtained from backrub?
by Vedasheersh » Wed, 2017-06-14 10:26 		5
 4,474 by SenyorDrew
Fri, 2017-06-30 09:47
Normal topic protein-protein docking with flexible backbone
by tim » Fri, 2013-12-20 05:52 		1
 4,490 by rmoretti
Mon, 2014-04-21 06:48
Normal topic xyzVector error in Enzyme design
by ajmbarbosa » Tue, 2016-01-05 09:46 		3
 4,499 by rmoretti
Fri, 2016-06-17 10:36
Normal topic comparative modelling and broker
by felipet » Tue, 2013-02-05 08:33 		4
 4,505 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06 		6
 4,506 by chandana
Tue, 2022-08-09 20:27
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43 		3
 4,512 by bjharris
Sun, 2020-08-23 14:03
Normal topic comparative modeling of protein-ligand complex
by tevang » Mon, 2013-09-09 09:06 		3
 4,520 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Rosetta RNA denovo huge memory usage (probable memory leak)
by cdegut » Mon, 2017-10-30 16:41 		5
 4,526 by cdegut
Fri, 2017-11-03 05:50
Normal topic Error when running Remodel with EnzDes constraint file to extend c-terminal
by Jeffrey_Chen » Thu, 2017-01-19 06:20 		4
 4,533 by dfcoelho
Tue, 2017-10-17 11:52
Normal topic AbinitioRelax Disulfide Bonds are not being retained
by brspurri » Wed, 2011-09-28 13:55 		1
 4,561 by parmef
Mon, 2014-04-21 06:47
Normal topic pmut_scan does not produce log file
by fglaser » Wed, 2013-10-16 07:25 		3
 4,569 by matteoferla
Tue, 2018-10-30 02:54
Normal topic Pepspec Errors running 3.4
by rrphenix » Tue, 2013-05-28 12:08 		4
 4,576 by rmoretti
Mon, 2014-04-21 06:47
Normal topic cluster.mpi running in MPI mode?
by sacch » Fri, 2011-11-18 23:30 		2
 4,576 by sacch
Mon, 2014-04-21 06:47
Normal topic homology modeling- Error: length mismatch between sequence and alignment.
by pdbb » Mon, 2012-10-01 07:57 		2
 4,578 by pdbb
Mon, 2014-04-21 06:47
Normal topic The confussion about an example in tutorial in Rosetta Virtual Workshop 2020
by ldx022 » Tue, 2022-11-29 04:58 		3
 4,585 by ldx022
Tue, 2022-11-29 08:38
Normal topic fragment_picker with fasta only
by gw » Tue, 2011-11-15 13:20 		3
 4,605 by gw
Mon, 2014-04-21 06:47
Normal topic Snugdock_input
by luicui » Wed, 2017-01-18 16:48 		5
 4,613 by smlewis
Fri, 2017-01-20 08:14
Normal topic Protein-DNA Docking using RosettaScripts?
by brspurri » Fri, 2013-06-07 09:06 		1
 4,640 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ddg monomer vs pmut scan
by dave » Tue, 2014-03-04 10:18 		3
 4,642 by smlewis
Fri, 2014-03-07 13:02
Normal topic InterfaceAnalyzer dSasa calculation
by mintseris » Wed, 2015-09-02 09:43 		2
 4,653 by jadolfbr
Thu, 2015-09-03 16:18
Normal topic Rosetta DNA - Protein-DNA scoring function and binding energy
by tanoramb » Tue, 2012-05-08 14:00 		1
 4,677 by smlewis
Mon, 2014-04-21 06:47
Normal topic conway2016 correction on beta-nov15?
by attesor » Wed, 2017-03-15 05:26 		5
 4,680 by attesor
Thu, 2017-03-16 01:21
Normal topic Discrepancy between the total pose energy and sum of per residue energies
by vijayan » Tue, 2013-07-02 07:24 		3
 4,682 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ERROR: no fragment to compute secondary structure
by byin » Sun, 2011-08-07 23:55 		3
 4,692 by smlewis
Mon, 2014-04-21 06:47
Normal topic Docking structures with ligands in cryo-EM maps
by galushin » Wed, 2012-07-11 12:40 		1
 4,707 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49 		4
 4,721 by sacch
Mon, 2014-04-21 06:47
Normal topic Syntax for the alignment file in "minirosetta comparative modeling"
by lanselibai » Thu, 2014-10-16 15:29 		3
 4,726 by lanselibai
Thu, 2014-10-23 03:26
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46 		2
 4,735 by libai2098
Mon, 2014-04-21 06:47
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26 		2
 4,741 by tingting
Tue, 2022-03-15 23:55
Normal topic Homology Modelling with cofactors
by Derek Smith » Thu, 2015-07-09 08:24 		3
 4,751 by Derek Smith
Wed, 2016-02-03 05:47
Normal topic Warning messages in Interface analyzer output
by Pernille » Wed, 2015-03-25 00:53 		4
 4,757 by rmoretti
Tue, 2015-03-31 08:20
Normal topic terminal amino acids of gap has incomplete valency
by malkeet.singh » Wed, 2017-11-29 05:20 		6
 4,777 by rmoretti
Fri, 2017-12-01 12:05
Normal topic Ligand atom RMSD calculation
by lkrathn » Wed, 2013-08-14 21:25 		2
 4,826 by lkrathn
Mon, 2014-04-21 06:48
Normal topic Positive scores with SymmDock in helical symmetry
by kxiao » Tue, 2014-02-11 07:37 		4
 4,843 by kxiao
Thu, 2014-06-05 08:37
Normal topic Error when running cluster
by aloshbau » Wed, 2013-05-01 20:45 		3
 4,860 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problems with always_constrained_relax_script
by wsgosal » Wed, 2013-05-29 04:39 		3
 4,901 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Symmetric Minimization
by aroop » Mon, 2012-12-17 11:45 		5
 4,922 by aroop
Mon, 2014-04-21 06:47
Normal topic FlexPepDocking with GDP-bound protein
by LI » Sun, 2011-06-12 20:02 		3
 4,925 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Can I assume the outputs from different runs are from a same batch?
by lanselibai » Mon, 2014-11-03 06:34 		4
 4,926 by lanselibai
Mon, 2014-11-03 13:15
Normal topic Rosetta ScriptsFeatures Reporter issue
by David Weis » Sun, 2017-03-12 08:19 		5
 4,935 by David Weis
Mon, 2017-03-13 10:59
Normal topic cyclization_type flag in simple_cycpep_predict
by Florent Langenfeld » Thu, 2018-01-04 09:22 		5
 4,968 by Florent Langenfeld
Tue, 2018-03-27 11:44
Normal topic sam.predict-2nd for make_fragments.pl script
by sumukh21 » Thu, 2011-02-17 12:29 		3
 4,972 by fukamitka
Mon, 2014-04-21 06:47
Normal topic favor native residue in fixBB design
by ast » Mon, 2012-12-10 06:00 		4
 4,986 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ligand docking and protein design of an internal pocket in a protein with a cofactor
by oerbilgin » Mon, 2011-06-20 13:55 		2
 4,988 by frichter
Mon, 2014-04-21 06:47
Normal topic Re: Glutamic acid protonation
by bharat_46010 » Fri, 2017-02-10 03:08 		4
 4,995 by rmoretti
Mon, 2017-02-20 08:09
Normal topic ReplicaDock 2.0 Native vs Input Structure Flags Confusion
by katherinemccoy » Tue, 2022-12-27 06:42 		2
 4,999 by katherinemccoy
Tue, 2023-02-28 18:19
Normal topic Different scoring applications (score vs score_aln vs score_jd2, etc.)?
by cossio » Fri, 2014-12-26 07:19 		3
 5,015 by Patrícia Antunes
Fri, 2023-01-20 11:55
Normal topic modeling an extracellular loop of a transmembrane protein
by Hothman » Fri, 2016-08-12 06:16 		5
 5,020 by rmoretti
Mon, 2016-09-05 10:59
Normal topic RosettaCM Tutorials
by smathersc » Wed, 2017-01-11 15:59 		5
 5,031 by rmoretti
Thu, 2017-01-19 09:11
Normal topic assymetric dymer modelling with comparative and ab initio
by marcia » Mon, 2013-10-14 08:33 		3
 5,044 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Local docking: "manually place the two proteins facing each other" ?
by mdeklotz » Fri, 2018-07-20 10:24 		5
 5,051 by dfcoelho
Tue, 2018-10-16 09:05
Normal topic Loop modeling - the appropriate way to model a peptide insertion?
by xding » Thu, 2018-08-02 15:30 		6
 5,073 by smlewis
Wed, 2018-08-08 15:48
Normal topic [TopologyBroker Exception]: BBTorsion at pos 468unitialized...unclaimed
by tevang » Wed, 2013-04-10 15:07 		5
 5,077 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40 		4
 5,101 by cossio
Mon, 2015-01-19 07:10
Normal topic make_rot_lib issue
by jarek » Thu, 2013-04-11 08:21 		4
 5,118 by smlewis
Mon, 2014-04-21 06:47
Normal topic Abrelax - Dunbrack02.lib.bin missing
by omirus » Sun, 2011-09-18 06:30 		3
 5,118 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ligand Docking with Rosetta Scripts memory problem
by Swillard » Thu, 2017-08-17 14:59 		5
 5,123 by rmoretti
Mon, 2018-11-12 14:31
Normal topic InterfaceAnalyzer problem
by almeida » Mon, 2014-03-03 14:56 		3
 5,140 by smlewis
Fri, 2014-03-07 14:09
Normal topic fixbb and ncaa's
by jarek » Thu, 2012-11-08 04:55 		4
 5,152 by jcminerlanl
Thu, 2017-12-21 10:13
Normal topic jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease
by fradom » Mon, 2017-11-27 02:55 		6
 5,165 by fradom
Tue, 2017-12-05 01:52
Normal topic clean_pdb.py of Rosetta VS cleanATOM of PyRosetta
by lanselibai » Wed, 2014-09-24 03:02 		2
 5,167 by lanselibai
Wed, 2014-09-24 13:21
Normal topic Homodimer interface design
by petrikigor » Fri, 2012-11-16 10:57 		3
 5,171 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Antibody modeling
by Maryam_tabasinezhad » Fri, 2015-09-04 11:00 		4
 5,172 by rmoretti
Wed, 2015-09-09 12:08
Normal topic RosettaAntibody
by mpendleton » Mon, 2011-04-04 10:27 		3
 5,176 by jianqing
Mon, 2014-04-21 06:47
Normal topic a question about ligand docking
by yzhou » Wed, 2012-05-30 18:57 		5
 5,181 by yzhou
Mon, 2014-04-21 06:47
Normal topic Disulfide prediction from primary sequence
by zcrook » Wed, 2014-11-12 14:44 		2
 5,200 by zcrook
Tue, 2014-11-25 10:27
Normal topic ddg_monomer conformational search...
by yperez » Wed, 2012-05-09 11:10 		5
 5,201 by yperez
Mon, 2014-04-21 06:47
Normal topic extract_pdbs fails to open silent file when -auto_setup_metals enabled
by attesor » Thu, 2015-01-15 03:22 		4
 5,203 by attesor
Tue, 2015-01-27 02:20
Normal topic fa_plane enregy term in scoring weights
by ytao » Fri, 2012-11-30 20:25 		4
 5,210 by smlewis
Mon, 2014-04-21 06:47
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09 		3
 5,220 by Sajjad
Wed, 2022-11-30 11:50
Normal topic pair energies across interface
by irini » Fri, 2012-02-10 09:17 		5
 5,235 by Anonymous
Mon, 2014-04-21 06:47
Normal topic ligand_docking_analysis
by Prasanth Kumar » Thu, 2013-05-09 23:51 		4
 5,250 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaCM -weights, fragments and relax
by jsv » Tue, 2017-05-09 10:20 		5
 5,256 by rmoretti
Thu, 2017-06-01 08:52
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32 		2
 5,271 by lanselibai
Thu, 2014-11-20 02:15
Normal topic Error while running RosettaLigand
by Ryhon Wang » Tue, 2013-07-30 02:51 		4
 5,277 by Ryhon Wang
Mon, 2014-04-21 06:48
Normal topic Missing common atom definitions in constraints
by ic3reyes » Sat, 2011-06-11 13:09 		3
 5,282 by smlewis
Mon, 2014-04-21 06:47
Normal topic minirosetta: weird behavior
by fred » Wed, 2014-01-22 05:57 		4
 5,292 by fred
Mon, 2014-04-21 06:48