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Rosetta 3 - Applications

Topic / Topic starter Repliessort ascending Views Last post
Normal topic modeling phosphorylated residue
by rosetter » Fri, 2011-03-18 08:13 		7
 8,888 by smlewis
Mon, 2014-04-21 06:47
Normal topic neutral N-term and C-term
by nawsad » Sun, 2013-06-09 10:20 		7
 9,389 by helenah
Thu, 2020-10-08 05:29
Normal topic Abinitio Relax Error from -kill_hairpins
by attesor » Tue, 2014-10-28 05:33 		7
 7,887 by rmoretti
Tue, 2014-11-04 10:28
Normal topic Inserting residues using RosettaRemodel
by eleishaj » Tue, 2015-11-24 08:54 		7
 8,828 by eyong123
Wed, 2015-12-09 07:17
Normal topic where is pdb2vall.py
by tevang » Thu, 2013-01-24 13:35 		7
 7,345 by dktest
Mon, 2014-04-21 06:47
Normal topic How to write down a connection between ligand's atom and metal ion from enzyme?
by Corvin » Mon, 2021-02-15 06:54 		7
 3,865 by aloshbau
Mon, 2021-03-01 20:06
Normal topic suppress pdb output from backrub
by attesor » Mon, 2014-10-27 11:16 		7
 7,494 by rmoretti
Mon, 2014-11-03 15:47
Normal topic Rosetta scoring
by Dimitrov » Thu, 2012-09-20 01:54 		7
 10,275 by attesor
Mon, 2014-04-21 06:47
Normal topic If "clustering.py" can be used for PDBs contain two chains?
by lanselibai » Wed, 2014-11-05 06:05 		7
 7,453 by lanselibai
Tue, 2014-12-02 09:43
Normal topic segmentation fault after core.kinematics.FoldTree in homology modeling
by pdbb » Mon, 2012-10-08 14:27 		7
 7,807 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Ensemble Docking in Rosetta3.5?
by protos_heis » Fri, 2015-05-22 06:42 		7
 8,895 by protos_heis
Mon, 2015-06-08 07:00
Normal topic "ddg_monomer.linuxgccrelease" by following "High Resolution Protocol"
by lanselibai » Wed, 2014-10-01 09:54 		7
 11,179 by lanselibai
Sat, 2015-01-03 08:18
Normal topic Relax a structure with >1 copy of a modified residue fails [Solved]
by franfdez » Wed, 2012-02-08 00:47 		6
 6,704 by franfdez
Mon, 2014-04-21 06:47
Normal topic ligand docking, how to combine some silent.out files into a silent_all.out file
by Ryhon Wang » Fri, 2013-12-06 01:53 		6
 7,593 by rmoretti
Wed, 2017-01-11 12:53
Normal topic How to model missing residues on a protein from multiple PDB files?
by cossio » Fri, 2015-08-21 07:18 		6
 13,676 by rmoretti
Fri, 2015-09-11 13:27
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 How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06 		6
 4,500 by chandana
Tue, 2022-08-09 20:27
Normal topic symmetric design in the presence of a nonsymmetric ligand
by msardejani » Fri, 2016-09-30 15:17 		6
 6,476 by msardejani
Sat, 2016-10-01 12:55
Normal topic the ddg of mutant is same as the wt
by deepanshuiitb » Wed, 2015-03-04 11:56 		6
 6,978 by jadolfbr
Tue, 2015-04-07 10:50
Normal topic Make error during installation of updated ncbi-blast-2.9.0+-src plus error with nr-database
by Corvin » Tue, 2019-10-01 02:04 		6
 6,558 by Corvin
Tue, 2019-10-15 01:12
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 CS-HM-Rosetta
by pwurm » Thu, 2013-03-07 12:56 		6
 7,402 by Marius1987
Fri, 2016-02-05 07:20
Normal topic the flexpepdock refinement and ab-initio
by tfliu » Mon, 2013-12-23 19:17 		6
 6,675 by tfliu
Mon, 2014-04-21 06:48
Normal topic Error src/core/scoring/MembraneTopology.cc line: 139
by Daniel Hall » Thu, 2017-07-13 04:58 		6
 6,233 by rmoretti
Tue, 2017-07-18 09:00
Normal topic Translate mover chain X doesnot exist.
by surya » Thu, 2020-07-09 08:36 		6
 3,601 by rmoretti
Tue, 2020-07-14 10:54
Normal topic enzyme design and output_matchres_only
by petrikigor » Wed, 2012-10-24 18:45 		6
 5,508 by petrikigor
Mon, 2014-04-21 06:47
Normal topic Abinitio doesn't run but does not give output or error
by Irving » Fri, 2016-10-28 10:04 		6
 6,099 by rmoretti
Mon, 2017-01-23 08:52
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 fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
by yueyuedake » Wed, 2023-07-12 03:36 		6
 1,414 by yueyuedake
Sun, 2023-07-16 19:17
Normal topic loop modeling during enzyme design?
by lzx32 » Wed, 2011-11-16 00:30 		6
 6,277 by lzx32
Mon, 2014-04-21 06:47
Normal topic Can I believe the antibody design result?
by Sunyp_IM » Mon, 2020-11-30 03:29 		6
 3,496 by jadolfbr
Sun, 2020-12-06 17:41
Normal topic RosettaLigand - strange score behavior
by Gerdes » Mon, 2014-02-03 02:24 		6
 7,182 by Gerdes
Fri, 2014-02-07 06:48
Normal topic Can't generate a cst file to use with ddg_monomer application
by ctqwong » Sat, 2021-03-13 03:53 		6
 3,257 by ctqwong
Thu, 2021-03-18 02:04
Normal topic EMERALD method not working, Rosetta version not available for download
by seba » Thu, 2023-05-04 08:14 		6
 1,858 by rmoretti
Mon, 2023-07-10 08:57
Normal topic Enzdes score file discrepancy between generated pdb and scores.out
by eyong123 » Wed, 2015-03-25 08:52 		6
 7,592 by eyong123
Mon, 2015-06-29 04:44
Normal topic Problems with ligand when running RosettaLigand
by Cat » Mon, 2013-05-20 15:58 		6
 7,410 by Aben
Tue, 2023-04-18 01:31
Normal topic Enzyme design with variable CST blocks possible?
by petrikigor » Thu, 2011-10-06 11:24 		6
 7,477 by petrikigor
Mon, 2014-04-21 06:47
Normal topic Results of enzyme_design not consistent with Resfile
by yogeshkd » Thu, 2013-02-14 15:56 		6
 6,806 by yogeshkd
Mon, 2014-04-21 06:47
Normal topic pepspec anchor dock
by Astghik » Tue, 2020-10-20 05:31 		6
 3,795 by Pappmaschee
Thu, 2020-12-17 02:24
Normal topic Incorrect Jump being set in RosettaScripts docking mover
by weehee » Fri, 2012-06-08 10:23 		6
 7,907 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Rotamers used in fixbb
by lanselibai » Thu, 2014-11-06 02:47 		6
 6,389 by lanselibai
Tue, 2014-11-11 15:28
Normal topic rosetta_2013wk52: make_fragments.pl failed
by fred » Thu, 2014-01-30 12:41 		6
 8,878 by rmoretti
Fri, 2014-02-07 08:01
Normal topic scoring of beta sandwich protein
by attesor » Mon, 2014-11-17 08:24 		6
 6,344 by rmoretti
Thu, 2014-11-20 10:46
Normal topic Comparative modeling stops with "no more batches to process... " / no output
by eskici » Tue, 2012-08-28 12:13 		6
 6,543 by eskici
Mon, 2014-04-21 06:47
Normal topic mover "RepackMinimize" does not support chains > 2?
by jarod » Mon, 2013-05-20 02:17 		6
 7,746 by jarod
Mon, 2014-04-21 06:47
Normal topic Abinitio (3.4) Error: no fragment to compute secondary structure
by skovacs » Tue, 2012-09-18 13:49 		6
 7,883 by skovacs
Mon, 2014-04-21 06:47
Normal topic How to define pi-pi stacking in cst file?
by lzx32 » Mon, 2011-07-04 23:47 		6
 8,430 by lzx32
Mon, 2014-04-21 06:47
Normal topic Docking with constraints
by ytao » Tue, 2013-04-02 09:45 		6
 8,229 by smlewis
Mon, 2014-04-21 06:47
Normal topic Line search failed even after resetting Hessian
by Loki01 » Wed, 2017-12-13 16:52 		6
 6,301 by Loki01
Thu, 2018-02-15 13:54
Normal topic Problem with hotspot constraints.
by jarek » Wed, 2012-10-17 03:22 		6
 6,083 by xfliu
Mon, 2014-04-21 06:47
Normal topic Missing "Bio.PDB" module when running "remove_loop_coords.py"
by lanselibai » Mon, 2014-09-29 04:34 		6
 10,574 by lanselibai
Wed, 2014-10-01 02:13
Normal topic Is Biopython required to run pdb_renumber.py?
by ljjjxay » Wed, 2023-11-22 20:00 		6
 1,131 by ljjjxay
Wed, 2023-12-06 19:24
Normal topic protein docking failed
by albumns » Thu, 2012-11-08 02:59 		6
 6,418 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ab inito memberane(error in alignblast.pl)
by kingljy » Tue, 2011-05-03 23:41 		6
 7,371 by karthishanmugam
Mon, 2014-04-21 06:47
Normal topic "sparks failed" error when running "make_fragments.pl"?
by Danielsebas » Tue, 2019-09-03 03:43 		6
 4,378 by Jacob_Verburgt
Tue, 2020-03-10 14:39
Normal topic Help with enzyme design
by lzx32 » Fri, 2011-04-08 22:29 		6
 6,828 by lzx32
Mon, 2014-04-21 06:47
Normal topic docking in rosetta 3.3
by Ammu » Thu, 2012-03-15 12:03 		6
 6,330 by smlewis
Mon, 2014-04-21 06:47
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 Cannot get a negative score after relax
by kxiao » Tue, 2014-01-28 22:28 		6
 8,081 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Distinctions between InterfaceAnalyzer and RosettaScript
by achambe » Wed, 2015-06-17 10:14 		6
 8,856 by rmoretti
Wed, 2015-09-02 12:43
Normal topic FloppyTail :How to specify range of design(mutation)
by syoifczeri » Mon, 2015-11-02 04:14 		6
 6,746 by syoifczeri
Sat, 2015-11-07 21:42
Normal topic extract silent error - tag mismatch
by shrutikhare » Thu, 2014-04-03 00:13 		5
 7,197 by rmoretti
Mon, 2014-04-21 10:47
Normal topic Error with the mpi version of simple_cycpep_predict
by Florent Langenfeld » Wed, 2020-02-05 05:16 		5
 3,435 by vmulligan
Fri, 2020-04-10 02:54
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 Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
by Danielsebas » Mon, 2019-09-23 03:24 		5
 3,429 by smlewis
Mon, 2019-09-23 11:42
Normal topic -score_app:linmin flag not working
by fglaser » Tue, 2011-03-01 06:04 		5
 5,813 by smlewis
Mon, 2014-04-21 06:47
Normal topic PDB format for RosettaDNA
by brspurri » Thu, 2013-05-30 11:21 		5
 6,665 by brspurri
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 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 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 Cartesian-space refinement
by sjyang7 » Wed, 2017-05-31 19:34 		5
 5,941 by sjyang7
Sat, 2017-06-03 06:09
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 Enzdes: increase weight of energy term for steric clashes with ligand
by eyong123 » Wed, 2015-03-25 09:12 		5
 6,338 by rmoretti
Fri, 2015-04-24 12:02
Normal topic RosettaLigand: How to score native pose in protein-ligand docking experiment?
by Ryhon Wang » Tue, 2015-11-10 01:30 		5
 6,022 by Ryhon Wang
Mon, 2016-01-04 19:59
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 Memory Leak: Relax Density MPI RAM overusage kills process
by mmfarrugia » Sun, 2023-12-31 12:02 		5
 858 by mmfarrugia
Fri, 2024-01-12 10:35
Normal topic RosettaScripts LinkResidues
by Yero » Fri, 2019-05-17 05:26 		5
 4,435 by Yero
Thu, 2019-07-18 01:39
Normal topic domain:domain fusion
by felipet » Thu, 2017-06-15 13:13 		5
 5,782 by felipet
Fri, 2017-06-16 11:42
Normal topic Can the Rosetta Antibody Design (RAbD) protocol incorporate glycans?
by ccottrell » Tue, 2020-05-05 20:30 		5
 3,187 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic ab initio protein prediction using homologs
by justin » Mon, 2012-02-13 07:52 		5
 5,995 by justin
Mon, 2014-04-21 06:47
Normal topic Parse error while reading in XML file in ROSETTA Scripts
by rweisse » Fri, 2014-08-29 03:24 		5
 9,757 by a-eatemadi@razi...
Sun, 2017-08-06 03:49
Normal topic Rosetta dock irmsd
by Pernille » Sun, 2015-04-26 13:51 		5
 7,264 by rmoretti
Mon, 2015-10-12 15:10
Normal topic snugdock(sequence position requested was greater than the number of residues in the pose)
by lei » Thu, 2023-01-12 01:40 		5
 2,919 by lei
Fri, 2023-01-20 08:11
Normal topic [TopologyBroker Exception]: BBTorsion at pos 468unitialized...unclaimed
by tevang » Wed, 2013-04-10 15:07 		5
 5,076 by rmoretti
Mon, 2014-04-21 06:47
Normal topic too many constraints result in no output pose
by Yao Wu » Sun, 2012-11-18 23:45 		5
 6,345 by smlewis
Mon, 2014-04-21 06:47
Normal topic extract_pdb application parse error with silent file
by staciekim » Tue, 2017-08-22 12:39 		5
 6,093 by rmoretti
Thu, 2017-08-24 08:19
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 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 How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38 		5
 3,552 by danpf
Tue, 2020-05-12 10:58
Normal topic Scoring functions: talaris2013 incompatible versions
by Smbat » Tue, 2020-10-13 06:18 		5
 3,388 by Astghik
Thu, 2020-10-15 00:48
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35 		5
 5,429 by rmoretti
Mon, 2015-02-09 12:04
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40 		5
 5,480 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic rosetta protein protein docking start up
by vk » Fri, 2011-06-24 09:01 		5
 7,351 by smlewis
Mon, 2014-04-21 06:47
Normal topic ndruns and nstruct in fixbb
by Anonymous » Tue, 2012-08-07 01:52 		5
 6,575 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Steric clashes in RNA minimization
by brianmlee » Tue, 2014-11-18 18:29 		5
 6,385 by brianmlee
Mon, 2014-11-24 19:40
Normal topic Symmetric Minimization
by aroop » Mon, 2012-12-17 11:45 		5
 4,921 by aroop
Mon, 2014-04-21 06:47
Normal topic ddg_monomer conformational search...
by yperez » Wed, 2012-05-09 11:10 		5
 5,200 by yperez
Mon, 2014-04-21 06:47
Normal topic How do you use two patches simulataneously with ab initio folding?
by smiruthi » Wed, 2011-12-21 15:24 		5
 5,604 by wangyr
Mon, 2014-04-21 06:47
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 a question about ligand docking
by yzhou » Wed, 2012-05-30 18:57 		5
 5,181 by yzhou
Mon, 2014-04-21 06:47