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Rosetta 3 - Applications

Topic / Topic starter Replies Viewssort descending Last post
Normal topic What is interface_cutoff_distance? And why did my residues outside this value get designed?
by chrisHKL » Fri, 2020-02-28 14:52
0
450 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
456 by chenna
Mon, 2021-04-12 22:08
Normal topic polymer docking using rosetta scripts
by syntekabio2019 » Fri, 2020-11-27 01:51
1
456 by rmoretti
Fri, 2020-11-27 10:47
Normal topic Extracting top score PIPER models
by almeida85 » Mon, 2020-08-31 07:17
0
465 by almeida85
Mon, 2020-08-31 07:17
Normal topic Can remodel really handle multiple insertions in one simulation?
by lanselibai » Sat, 2019-12-28 12:51
0
467 by lanselibai
Sat, 2019-12-28 12:51
Normal topic Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms
by Corvin » Wed, 2020-12-02 04:00
1
468 by rmoretti
Wed, 2020-12-02 07:27
Normal topic Flex_ddG crashes when attempting to move 2 chains (e.g. chains_to_move = A,C)
by jcampecino » Wed, 2020-05-13 12:22
0
469 by jcampecino
Wed, 2020-05-13 12:22
Normal topic score is 0 in the output? - RosettaScripts
by chrisHKL » Thu, 2020-03-05 09:33
0
470 by chrisHKL
Thu, 2020-03-05 12:58
Normal topic Comparative Modeling Templates for Protein with Multiple Domains
by Morrian_Lynn » Wed, 2020-03-04 10:42
0
471 by Morrian_Lynn
Wed, 2020-03-04 10:42
Normal topic Using Rmsd RosettaScripts filter with alignment files
by bjharris » Sun, 2020-11-08 15:51
1
473 by rmoretti
Sun, 2020-11-08 18:56
Normal topic antibody.mpi.linuxgccrelease some antibodies failing to model
by drewaight » Mon, 2020-11-02 17:07
0
475 by drewaight
Mon, 2020-11-02 17:07
Normal topic NCAA Rotamers for Cyclosporin
by marinok » Mon, 2020-09-28 14:11
0
480 by marinok
Mon, 2020-09-28 14:11
Normal topic Error from clean_pdb.py
by code_Monkey » Mon, 2021-03-01 17:00
2
491 by code_Monkey
Thu, 2021-03-04 12:14
Normal topic antibody H3 modelling protocol for nanobody gives "[ ERROR ] Inaccurate G!" messages
by AlfredoKCL » Sun, 2021-02-28 16:42
2
494 by AlfredoKCL
Mon, 2021-03-01 04:07
Normal topic Pepspec Anchor Dock
by Soler » Fri, 2020-09-18 08:09
0
499 by Soler
Fri, 2020-09-18 08:09
Normal topic Limit on backbone movement in relax?
by SWM » Fri, 2020-01-24 07:35
0
501 by SWM
Fri, 2020-01-24 07:35
Normal topic Modeling-Using RosettaCM
by jlawrie » Wed, 2020-08-12 08:46
1
503 by jlawrie
Wed, 2020-08-12 08:47
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
0
503 by CATarr
Wed, 2019-10-09 19:05
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
0
505 by linhhoang157
Tue, 2020-07-28 12:40
Normal topic Input structure
by Soler » Mon, 2020-09-28 13:18
1
507 by ssrb
Tue, 2020-09-29 12:37
Normal topic Use membrane or non-membrane weights in RosettaCM for a hexon in virus capsid?
by lanselibai » Sat, 2020-04-11 02:10
0
508 by lanselibai
Sat, 2020-04-11 02:10
Normal topic Rosetta remodel - including an RNA ligand
by daniloboskovic » Fri, 2020-04-10 04:24
0
510 by daniloboskovic
Fri, 2020-04-10 04:24
Normal topic Membrane Abinitio modeling error
by jkyan007 » Thu, 2020-10-29 03:30
1
511 by noahC_noahDo
Tue, 2020-11-17 10:35
Normal topic Problems with mpi version of antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 23:06
0
516 by Sunyp_IM
Thu, 2020-05-28 23:07
Normal topic Protein Ensemble RosettaLigand Docking
by sam_dc » Fri, 2021-03-26 10:18
2
516 by sam_dc
Fri, 2021-03-26 12:04
Normal topic AbinitioRelax detect_disulf_tolerance
by aarono » Tue, 2020-06-02 00:13
0
519 by aarono
Tue, 2020-06-02 00:13
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
0
521 by wentlewi
Fri, 2020-03-13 03:24
Normal topic RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()
by sam_dc » Thu, 2021-03-25 09:32
2
524 by sam_dc
Mon, 2021-04-12 07:24
Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
525 by leygkn
Tue, 2020-09-22 22:46
Normal topic Docking the border segments of coiled coils in parallel orientation
by Corvin » Mon, 2019-12-02 02:00
0
528 by Corvin
Mon, 2019-12-02 02:00
Normal topic What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001."
by Corvin » Thu, 2020-04-02 00:16
0
529 by Corvin
Thu, 2020-04-02 00:16
Normal topic [Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence
by brspurri » Mon, 2021-01-04 16:46
1
534 by brspurri
Mon, 2021-01-18 18:14
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
1
541 by ssrb
Mon, 2020-06-22 13:12
Normal topic Error Implementing Match Style Constraints
by pwging13 » Thu, 2019-12-19 09:53
0
542 by pwging13
Thu, 2019-12-19 09:53
Normal topic core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard
by AlfredoKCL » Sat, 2020-11-07 18:21
0
548 by AlfredoKCL
Sat, 2020-11-07 18:21
Normal topic how to run ala_scan.xml
by xinmiaohe » Mon, 2019-08-26 09:38
0
548 by xinmiaohe
Mon, 2019-08-26 09:38
Normal topic 'standard.wts' does not exist
by almeida85 » Mon, 2020-09-14 02:26
1
550 by rmoretti
Mon, 2020-09-14 06:36
Normal topic new BUNS for FunFolDes run
by tatsiana.bylund » Wed, 2019-08-14 20:57
0
558 by tatsiana.bylund
Wed, 2019-08-14 20:57
Normal topic using DARC in rosetta
by syntekabio2019 » Thu, 2019-12-12 01:27
0
561 by syntekabio2019
Thu, 2019-12-12 01:27
Normal topic help surface_docking peptide on ice
by engand93 » Wed, 2019-03-27 02:43
0
564 by engand93
Wed, 2019-03-27 02:43
Normal topic RNP structure prediction flags
by daniloboskovic » Fri, 2019-08-16 11:10
0
568 by daniloboskovic
Fri, 2019-08-16 11:17
Normal topic Changing rosetta scoring to favour less hydrophobic areas
by daniloboskovic » Thu, 2020-05-21 03:03
1
568 by vmulligan
Thu, 2020-05-21 18:33
Normal topic Docking of multichain oligomers
by sdh_h » Wed, 2020-03-25 12:43
0
569 by sdh_h
Wed, 2020-03-25 12:43
Normal topic cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues
by ValentinaSora » Sun, 2020-05-24 12:32
0
574 by ValentinaSora
Sun, 2020-05-24 12:32
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
1
575 by Andre Serobian
Tue, 2020-07-28 23:26
Normal topic Constraint generator
by Alison_Yajie » Wed, 2020-06-17 20:14
1
584 by Alison_Yajie
Wed, 2020-06-17 20:35
Normal topic Multistate design issues with -run:msd_job_dist option and MSDMover
by elaine.thai » Wed, 2020-05-13 18:07
0
584 by elaine.thai
Wed, 2020-05-13 18:07
Normal topic structure prediction
by MA » Wed, 2018-09-05 00:50
0
584 by MA
Wed, 2018-09-05 00:50
Normal topic mp_transform optimize with franklin2019 scoring
by benhardy » Thu, 2020-05-28 08:35
0
588 by benhardy
Thu, 2020-05-28 08:45
Normal topic extract docking pose from ligand docking silent file
by Ruska322 » Sat, 2019-09-07 05:21
0
595 by Ruska322
Sat, 2019-09-07 05:21
Normal topic Rosetta Ligand Ensemble
by malfonsoprieto » Wed, 2021-05-26 10:21
3
599 by vizcarra
Thu, 2021-08-26 10:16
Normal topic denovo_density don't output a pdb file
by ylwang » Sun, 2018-11-18 17:51
0
600 by ylwang
Sun, 2018-11-18 17:51
Normal topic protein-ligand docking rescoring with interfaceAnalyzer
by syntekabio2019 » Sat, 2020-12-19 03:59
2
601 by syntekabio2019
Sun, 2020-12-20 21:10
Normal topic Weighted scores??
by sizhang » Wed, 2018-12-05 15:22
0
601 by sizhang
Wed, 2018-12-05 15:22
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
603 by matteoferla
Mon, 2020-05-04 02:02
Normal topic manually defining CDRs in antibody modelling
by gard.nelson » Fri, 2020-07-10 13:31
1
607 by brspurri
Wed, 2021-01-20 08:11
Normal topic Warning: Fold tree is not set properly for density scoring
by ahansel » Mon, 2020-07-13 10:50
1
618 by danpf
Tue, 2020-07-14 10:27
Normal topic Ddg filter threshold value?
by chrisHKL » Fri, 2020-02-28 15:01
1
627 by rmoretti
Wed, 2020-03-04 09:56
Normal topic An error with score app
by Genta » Tue, 2019-10-29 18:46
0
632 by Genta
Tue, 2019-10-29 18:46
Normal topic How can I model ligands in comparative modeling
by Morrian_Lynn » Thu, 2020-02-20 09:57
1
633 by danpf
Fri, 2020-02-21 17:05
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
649 by ksteczk
Sat, 2020-04-11 11:23
Normal topic The difference between the H1 regions of modeled camelid antibody and the crystal structure.
by Sunyp_IM » Sun, 2020-06-07 02:34
1
651 by nannemdp
Sun, 2020-06-07 08:01
Normal topic How to add additional rounds of design and optimization in Rosetta scripts?
by Nicole Deng » Tue, 2020-11-03 19:05
2
653 by Nicole Deng
Thu, 2020-11-05 03:04
Normal topic using piper-flexpepdock
by syntekabio2019 » Thu, 2019-12-12 01:22
0
654 by syntekabio2019
Thu, 2019-12-12 01:22
Normal topic BuildPeptide - Using Phosphorylated and Sulfated Tyrosine
by jlawrie » Thu, 2020-09-03 14:29
1
661 by cryosky
Mon, 2021-03-01 21:37
Normal topic Error: in membrane docking : Cannot split pose by membrane jump! Quitting...
by Astghik » Tue, 2020-11-24 05:27
2
664 by Astghik
Thu, 2020-12-03 02:35
Normal topic can remodel add loops in one chain in multichain PDB structure?
by ksteczk » Fri, 2020-05-01 06:26
1
673 by matteoferla
Mon, 2020-05-04 01:43
Normal topic Symmetry mode in Remodel for N-terminal extension
by yvonne.chan2 » Mon, 2019-11-04 13:41
0
673 by yvonne.chan2
Mon, 2019-11-04 13:41
Normal topic PDB file name too long to be handled by file system
by dave » Thu, 2019-08-08 03:10
1
677 by rmoretti
Mon, 2019-08-26 12:17
Normal topic Energy function and iteration script files
by michelleqyh » Fri, 2019-09-27 09:06
1
680 by smlewis
Fri, 2019-09-27 11:54
Normal topic Thread target sequence
by duz » Thu, 2021-04-01 10:09
4
683 by duz
Mon, 2021-05-03 07:50
Normal topic remodel ERROR: unrecognized mm_atom_type_name RGU
by daniloboskovic » Sat, 2020-02-22 11:55
1
684 by daniloboskovic
Tue, 2020-02-25 08:28
Normal topic where is generate_ligens.linuxgccrelease?
by Nicole Deng » Thu, 2020-12-03 00:00
2
685 by Nicole Deng
Fri, 2020-12-18 00:28
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
685 by DGR95
Wed, 2021-04-28 16:13
Normal topic Flexpepdock I_hb scoring term
by mbakalar » Fri, 2018-08-31 13:05
0
687 by mbakalar
Fri, 2018-08-31 13:06
Normal topic Secondary Matching build_sets Error
by enmirts » Wed, 2018-03-28 10:33
0
689 by enmirts
Wed, 2018-03-28 10:34
Normal topic comparative modelling of a complex
by sdh_h » Sun, 2017-12-17 06:07
0
694 by sdh_h
Sun, 2017-12-17 06:07
Normal topic rosetta remodel and designing helix extension
by dhirajks » Thu, 2018-12-13 19:34
0
695 by dhirajks
Thu, 2018-12-13 19:34
Normal topic RosettaCM
by jlawrie » Fri, 2020-08-14 14:09
0
696 by jlawrie
Fri, 2020-08-14 14:09
Normal topic FASTA for Octopus
by Smbat » Wed, 2020-09-16 05:40
1
697 by rmoretti
Wed, 2020-09-16 22:11
Normal topic Strong bias in sampling observed in RosettaDock
by chenna » Thu, 2020-08-27 22:23
2
699 by chenna
Tue, 2021-10-12 20:51
Normal topic Problem with Scoring function and PlaceStub mover
by a-eatemadi@razi... » Sat, 2018-04-07 09:22
0
705 by a-eatemadi@razi...
Sat, 2018-04-07 09:24
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
0
706 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic Dock two domains using topology broker
by sn » Thu, 2017-10-05 17:07
0
711 by sn
Thu, 2017-10-05 17:07
Normal topic how to know the precedure of solving a actural bio problem? like interface design?
by qq7678500549 » Thu, 2020-08-06 18:45
2
711 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic /database folder after running "install_dependencies.pl" size 657 GB?
by Danielsebas » Tue, 2019-09-03 03:32
1
714 by danpf
Tue, 2019-09-03 10:15
Normal topic Do partner1 and partner2 in mover BackrubDD mean chain1 and chain2 respectively?
by johnnytam100 » Fri, 2019-08-23 21:10
1
715 by rmoretti
Mon, 2019-08-26 12:03
Normal topic hbond_sr_bb and hbond_lr_bb for different chains
by tylerborrman » Tue, 2020-10-13 13:41
2
718 by tylerborrman
Tue, 2021-02-09 16:33
Normal topic density scoring
by Tianyang89 » Sat, 2020-08-29 04:54
1
718 by danpf
Sun, 2020-08-30 22:23
Normal topic get an increased energy after energy minimization when using different score functions for repacking and energy minimization
by xinmiaohe » Fri, 2020-02-07 11:59
1
719 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic Loop modeling with constraints
by agctomer » Sat, 2021-03-20 03:53
3
720 by agctomer
Thu, 2021-04-08 07:37
Normal topic DDG and interaction score problem
by a-eatemadi@razi... » Mon, 2018-04-09 22:54
0
720 by a-eatemadi@razi...
Mon, 2018-04-09 22:54
Normal topic Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo
by zharmad » Fri, 2019-08-23 01:16
1
723 by everyday847
Fri, 2019-08-23 04:08
Normal topic Error when trying docking protocol with different ligand
by scyphs » Wed, 2020-08-05 04:37
2
727 by scyphs
Mon, 2020-08-10 08:09
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03
2
731 by jlawrie
Wed, 2020-08-12 07:27
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
738 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
743 by smlewis
Mon, 2019-09-16 12:22
Normal topic Protein-Protein Docking or Comparative Modeling
by Morrian_Lynn » Wed, 2020-01-29 19:01
1
745 by danpf
Fri, 2020-02-21 18:23
Normal topic fixing sequence during grafting in antibody_designer
by COM » Fri, 2020-01-24 11:38
1
746 by jadolfbr
Tue, 2020-01-28 09:13
Normal topic DDG_monomer ΔΔG question
by asbelx » Fri, 2018-04-20 03:31
0
757 by asbelx
Fri, 2018-04-20 03:33
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