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Rosetta 3 - Applications

Topic / Topic starter Replies Views Last postsort descending
Normal topic antibody H3 modelling protocol for nanobody gives "[ ERROR ] Inaccurate G!" messages
by AlfredoKCL » Sun, 2021-02-28 16:42
2
668 by AlfredoKCL
Mon, 2021-03-01 04:07
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
1,628 by aloshbau
Mon, 2021-03-01 20:06
Normal topic BuildPeptide - Using Phosphorylated and Sulfated Tyrosine
by jlawrie » Thu, 2020-09-03 14:29
1
775 by cryosky
Mon, 2021-03-01 21:37
Normal topic Error from clean_pdb.py
by code_Monkey » Mon, 2021-03-01 17:00
2
651 by code_Monkey
Thu, 2021-03-04 12:14
Normal topic Comparative Modeling Tutorial
by code_Monkey » Thu, 2021-03-04 12:35
1
504 by rmoretti
Fri, 2021-03-05 09:35
Normal topic Ab Initio folding with HEM ligand molecule
by jseco » Fri, 2021-03-05 06:49
0
378 by jseco
Mon, 2021-03-08 03:40
Normal topic Can't generate a cst file to use with ddg_monomer application
by ctqwong » Sat, 2021-03-13 03:53
6
1,369 by ctqwong
Thu, 2021-03-18 02:04
Normal topic Should I be stripping water molecules from my input structure for Rosetta Design?
by chrisHKL » Wed, 2021-03-24 14:22
1
515 by smlewis
Wed, 2021-03-24 14:59
Normal topic Protein Ensemble RosettaLigand Docking
by sam_dc » Fri, 2021-03-26 10:18
2
696 by sam_dc
Fri, 2021-03-26 12:04
Normal topic Can rosetta generate a centroid model based on the rna sequence?
by yels » Fri, 2021-03-26 04:06
7
1,388 by yels
Wed, 2021-03-31 18:31
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
521 by everyday847
Sun, 2021-04-04 12:48
Normal topic PDB Clustering
by code_Monkey » Mon, 2021-04-05 10:40
0
359 by code_Monkey
Mon, 2021-04-05 10:40
Normal topic Loop modeling with constraints
by agctomer » Sat, 2021-03-20 03:53
3
923 by agctomer
Thu, 2021-04-08 07:37
Normal topic Patch to impose tetrahedral geometry on backbone O atom
by georg » Thu, 2021-04-08 09:30
0
341 by georg
Thu, 2021-04-08 09:31
Normal topic issues about cstfile in RosettaMatch
by Nicole Deng » Fri, 2020-12-18 05:44
3
1,244 by He Xiao
Sun, 2021-04-11 19:29
Normal topic RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()
by sam_dc » Thu, 2021-03-25 09:32
2
758 by sam_dc
Mon, 2021-04-12 07:24
Normal topic What is an SS0 predictor?
by ojmel » Fri, 2021-04-02 14:25
0
328 by ojmel
Mon, 2021-04-12 07:50
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
617 by chenna
Mon, 2021-04-12 22:08
Normal topic r_frag_quality
by ii_cnr » Mon, 2021-04-12 03:06
2
591 by ii_cnr
Mon, 2021-04-12 23:44
Normal topic multi ligand docking using rosetta script
by syntekabio2019 » Tue, 2021-04-13 19:31
0
363 by syntekabio2019
Tue, 2021-04-13 19:31
Normal topic Docking Analysis and Metrics in RosettaLigand.
by sam_dc » Tue, 2021-04-20 03:54
1
655 by rmoretti
Tue, 2021-04-20 13:27
Normal topic Element 'trRosettaProtocol': This element is not expected.
by csaylan » Tue, 2021-04-20 14:21
2
623 by csaylan
Tue, 2021-04-20 16:13
Normal topic Filling the missing loops
by code_Monkey » Tue, 2021-04-27 07:44
2
588 by code_Monkey
Tue, 2021-04-27 12:11
Normal topic Generalized KIC loop closure affects downstream residues without perturbations
by chenna » Mon, 2021-04-26 02:16
2
605 by chenna
Wed, 2021-04-28 07:18
Normal topic RosettaCM/hybridize
by kywei » Wed, 2021-04-28 09:56
1
450 by vmulligan
Wed, 2021-04-28 12:59
Normal topic ligand_docking tutorial help: do crystal_complex.pdb files need to be prepped before using with <InterfaceScoreCalculator>
by DGR95 » Fri, 2021-04-16 19:26
4
936 by DGR95
Wed, 2021-04-28 16:13
Normal topic hpatch commands and how to identify patches
by Bianca Oliva » Thu, 2021-04-29 04:02
0
384 by Bianca Oliva
Thu, 2021-04-29 04:02
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
1
448 by rmoretti
Thu, 2021-04-29 10:44
Normal topic Score Functions for Ligand-protein Docking
by ziruiw » Sun, 2021-04-25 13:41
4
1,148 by ziruiw
Fri, 2021-04-30 12:01
Normal topic Thread target sequence
by duz » Thu, 2021-04-01 10:09
4
908 by duz
Mon, 2021-05-03 07:50
Normal topic trRosetta protocol Segmentation Fault
by nc-ring » Wed, 2021-04-28 11:57
5
1,121 by nc-ring
Tue, 2021-05-04 12:26
Normal topic Disulfide Bonds in Loop Modeling
by code_Monkey » Mon, 2021-05-03 08:27
2
633 by code_Monkey
Thu, 2021-05-06 07:14
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
0
331 by DGR95
Fri, 2021-05-14 12:51
Normal topic residue_energy_breakdown of a protein-ligand complex.
by sam_dc » Tue, 2021-05-18 04:45
1
480 by rmoretti
Tue, 2021-05-18 07:21
Normal topic FastRelax Refinement severe clashes
by Victor Tobiasson » Thu, 2021-05-20 06:55
0
351 by Victor Tobiasson
Thu, 2021-05-20 06:55
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:30
1
445 by taylorjones
Wed, 2021-06-09 16:38
Normal topic Fastsaxs
by Pernille » Mon, 2013-07-22 07:29
14
34,191 by rmoretti
Mon, 2021-06-14 12:56
Normal topic different value of score from rna_denovo and rna_score?
by yikanzhang » Wed, 2021-02-03 07:17
1
488 by CameronJA
Tue, 2021-06-15 20:02
Normal topic NCAA attached at two points
by tsztain » Wed, 2021-06-16 15:20
3
659 by matteoferla
Sat, 2021-06-19 03:07
Normal topic setup_RosettaCM.py
by browns02 » Mon, 2021-06-28 07:13
2
491 by browns02
Tue, 2021-06-29 11:41
Normal topic How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )
by asbelx » Sat, 2019-06-08 00:07
3
1,566 by happycaapi
Tue, 2021-06-29 15:35
Normal topic Repacker vs minimization
by Elijah_Hix » Fri, 2021-07-02 07:25
0
251 by Elijah_Hix
Fri, 2021-07-02 07:25
Normal topic D-amino acids tripeptide docking.
by sam_dc » Sat, 2021-07-03 08:48
2
559 by vmulligan
Tue, 2021-07-06 08:27
Normal topic rosetta_cm segfault
by browns02 » Fri, 2021-07-09 13:35
2
517 by rmoretti
Fri, 2021-07-09 15:05
Normal topic Running Rosetta CM Hybridize step errors with: Scorefunction not set up for nonideal/Cartesian scoring
by brspurri » Wed, 2017-03-29 13:19
7
4,078 by matteoferla
Mon, 2021-07-19 06:13
Normal topic FlexPepDock ab initio: behavior without fragment files
by nrollins » Mon, 2021-07-26 14:16
0
248 by nrollins
Mon, 2021-07-26 14:16
Normal topic FlexPepDock bug? Constraints do not appear in total_score?
by nrollins » Mon, 2021-07-26 14:29
0
291 by nrollins
Mon, 2021-07-26 14:29
Normal topic Stepwise Monte Carlo - errors with ResidueTypeSet and Disulfides
by user42 » Wed, 2021-07-21 20:34
1
398 by everyday847
Fri, 2021-07-30 13:26
Normal topic clashes created with enzdes
by listofdina » Mon, 2021-08-02 06:51
0
306 by listofdina
Mon, 2021-08-02 06:51
Normal topic Topobuilder segmentation fault
by tatsiana.bylund » Mon, 2021-08-09 07:10
0
469 by tatsiana.bylund
Mon, 2021-08-09 07:10
Normal topic duplex RNA
by amir_tagh » Thu, 2021-08-05 06:34
1
420 by everyday847
Mon, 2021-08-16 10:43
Normal topic Rosetta Ligand Ensemble
by malfonsoprieto » Wed, 2021-05-26 10:21
3
860 by vizcarra
Thu, 2021-08-26 10:16
Normal topic Missing atoms and cannot find atom pose when refining ligand position with EM density
by BuddySphinx » Mon, 2018-12-31 16:22
2
2,146 by e3lm
Tue, 2021-09-14 10:02
Normal topic Python2 script in Rosetta3.13
by ddhoyo » Wed, 2021-09-15 04:05
1
433 by matteoferla
Wed, 2021-09-15 06:04
Normal topic Error reading in/out glycosylated silent file - "Can't create a polymer bond after residue due to incompatible type"
by amorin » Mon, 2021-09-27 12:16
0
280 by amorin
Mon, 2021-09-27 12:16
Normal topic antibody - sequence position requested was 0
by jremmel » Mon, 2021-09-27 12:26
1
344 by nannemdp
Mon, 2021-09-27 14:22
Normal topic Symmetry definition file versions
by Jeff Qu » Tue, 2021-09-28 09:53
0
226 by Jeff Qu
Tue, 2021-09-28 09:53
Normal topic RoseTTaFold
by ozsolomon » Thu, 2021-10-07 05:27
2
687 by ozsolomon
Thu, 2021-10-07 14:25
Normal topic Linker Building in scFv
by sam_dc » Sat, 2021-10-09 05:38
0
229 by sam_dc
Sat, 2021-10-09 05:38
Normal topic Rosetta DARc suboptimal dockings
by ddhoyo » Mon, 2021-10-11 06:18
0
203 by ddhoyo
Mon, 2021-10-11 06:18
Normal topic Strong bias in sampling observed in RosettaDock
by chenna » Thu, 2020-08-27 22:23
2
848 by chenna
Tue, 2021-10-12 20:51
Normal topic building a protein-dna homology model via cm_rosetta
by y_atsmonraz » Wed, 2021-10-20 23:11
4
502 by y_atsmonraz
Tue, 2021-11-02 01:47
Normal topic connecting rna strands together
by y_atsmonraz » Tue, 2021-11-09 05:42
1
257 by y_atsmonraz
Thu, 2021-11-11 04:51
Normal topic C-termini remodelling of dimeric structure removes second chain
by LeonhardJS » Wed, 2021-10-13 06:23
1
311 by LeonhardJS
Fri, 2021-11-12 01:20
Normal topic The energy terms in InterfaceAnalyzer
by Sunyp_IM » Tue, 2021-11-02 18:43
2
357 by zivben
Sat, 2021-11-13 04:49
Normal topic Problems with waters in CoupledMoves application
by Corvin » Tue, 2021-11-16 07:16
0
259 by Corvin
Tue, 2021-11-16 07:22
Normal topic constraining different chains together in rosetta_cm
by y_atsmonraz » Thu, 2021-11-18 02:59
0
253 by y_atsmonraz
Thu, 2021-11-18 03:01
Normal topic ERROR: Unable to fill in missing atoms.
by mieczyslaw » Tue, 2020-10-20 09:43
7
2,863 by rayyoung
Thu, 2021-11-18 10:13
Normal topic SecundaryStructure Filter
by Soler » Sun, 2021-11-21 22:20
0
247 by Soler
Sun, 2021-11-21 22:20
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
0
180 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic Relaxed proteins show higher clash score in molprobity results.
by Wang Zhe » Fri, 2021-12-03 04:32
4
568 by smlewis
Wed, 2021-12-08 13:02
Normal topic Remodel's problem in treatment with non-protein residues
by Corvin » Mon, 2021-12-13 09:07
0
177 by Corvin
Mon, 2021-12-13 09:07
Normal topic Segfault error while running MR Rosetta in Phenix
by memilton » Thu, 2021-12-16 09:09
0
206 by memilton
Thu, 2021-12-16 09:09
Normal topic simple_cycpep_predict with N-term acetylation
by Ken » Fri, 2021-12-17 09:49
0
167 by Ken
Fri, 2021-12-17 09:49
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
452 by alonwenger
Sat, 2021-12-18 12:32
Normal topic Question about running scallo
by danbo » Mon, 2021-11-29 23:25
8
751 by danbo
Wed, 2021-12-22 23:51
Normal topic ERROR: APBS failed to generate the result file.
by bhavranek » Sat, 2021-12-18 11:01
1
236 by bhavranek
Sun, 2021-12-26 21:05
Normal topic [LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.
by dgm3 » Sun, 2021-12-26 18:32
1
246 by dgm3
Fri, 2021-12-31 17:42
Normal topic Protein design: Ligand binding between two units of a homodimer
by chemotaxis_123 » Sun, 2022-01-02 16:01
0
171 by chemotaxis_123
Sun, 2022-01-02 16:01
Normal topic I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes
by Wenithor » Thu, 2022-01-06 12:20
0
200 by Wenithor
Thu, 2022-01-06 12:20
Normal topic charge grid in rosetta ligand docking using rosetta script
by syntekabio2019 » Mon, 2022-01-17 23:53
0
200 by syntekabio2019
Mon, 2022-01-17 23:53
Normal topic ligand dock into HEM containg pdb
by syntekabio2019 » Thu, 2022-01-20 03:05
0
217 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic Can anybody suggests some flags to run Rifdock?
by Hyunmi Song » Sun, 2022-01-23 16:45
0
253 by Hyunmi Song
Sun, 2022-01-23 16:45
Normal topic Relax in membrane pull my protein out of the membrane
by Martin Floor » Wed, 2022-01-26 07:46
0
256 by Martin Floor
Wed, 2022-01-26 07:46
Normal topic FastRelaxMover parameters for antibody-antigen interaction analysis
by samuel_k » Thu, 2022-01-27 01:08
0
238 by samuel_k
Thu, 2022-01-27 01:08
Normal topic Generating the 3-mer and 9-mer fragments
by Prasoon » Wed, 2022-02-09 09:04
0
223 by Prasoon
Wed, 2022-02-09 09:04
Normal topic RAbD with N-term,Proline-like ncaa returns segmentation fault during CCDEndsGraftMover
by CordycepsLin » Sun, 2022-02-06 19:09
9
612 by CordycepsLin
Wed, 2022-02-09 19:39
Normal topic DockingProtocol
by Soler » Fri, 2022-02-11 00:12
3
362 by gezmi
Tue, 2022-02-15 21:47
Normal topic Using GlycanDock and the Antibody Affinity Maturation protocol.
by tbelec » Mon, 2022-02-28 12:37
0
177 by tbelec
Mon, 2022-02-28 12:37
Normal topic Rosetta Matcher not recognizing protonation forms of CST files like CYZ, HIS_D, etc
by Hirbond » Tue, 2022-03-01 13:16
0
148 by Hirbond
Tue, 2022-03-01 13:16
Normal topic small ligand docking in Ubuntu 20.04, please help
by guowuchen » Sun, 2022-03-06 18:12
2
232 by guowuchen
Mon, 2022-03-07 23:34
Normal topic simple_cycpep_predict thioether_lariat option
by Ken » Mon, 2022-03-14 15:14
0
114 by Ken
Mon, 2022-03-14 15:14
Normal topic Error in a new docking
by jrcf » Wed, 2017-05-17 19:26
2
2,735 by tingting
Tue, 2022-03-15 23:55
Normal topic RosettaDock 4.0 ambiguous ERROR
by sam_dc » Fri, 2022-03-18 09:36
3
231 by rmoretti
Tue, 2022-03-22 09:10
Normal topic Modelling at defined pH - for pmutscan - pH:mode not working
by cagfa1 » Tue, 2022-03-15 04:05
1
142 by Rituparna_Saman...
Wed, 2022-03-23 11:21
Normal topic How do I change the default Compiler for Rosetta?
by pagumaaaaa » Wed, 2022-03-16 00:23
2
204 by pagumaaaaa
Thu, 2022-03-24 22:40
Normal topic snugdock run error: Sequence for partner1 does not match first member of ensemble1
by pagumaaaaa » Fri, 2022-03-25 01:21
0
78 by pagumaaaaa
Fri, 2022-03-25 01:21
Normal topic problem in using "zinc_site_redesign" tool
by Isomerase » Mon, 2022-03-28 01:19
0
72 by Isomerase
Mon, 2022-03-28 01:19
Normal topic trRosetta - Nan occuring in Hbond calculation
by y_atsmonraz » Mon, 2021-10-04 09:16
1
235 by shivarawat115
Mon, 2022-04-11 16:10
Normal topic Ways to improve AbRelax performance?
by Corvin » Tue, 2022-04-19 06:10
2
139 by Corvin
Thu, 2022-04-21 00:50
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