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Rosetta 3 - Applications

Topic / Topic starter Replies Views Last postsort ascending
Normal topic Extracting top score PIPER models
by almeida85 » Mon, 2020-08-31 07:17
0
1,058 by almeida85
Mon, 2020-08-31 07:17
Normal topic density scoring
by Tianyang89 » Sat, 2020-08-29 04:54
1
1,917 by danpf
Sun, 2020-08-30 22:23
Normal topic RosettaAntibody3 - How can I model an extended H3?
by brspurri » Fri, 2020-08-28 09:11
0
898 by brspurri
Fri, 2020-08-28 09:11
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43
3
4,391 by bjharris
Sun, 2020-08-23 14:03
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
0
997 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic Successful RosettaCM?
by jlawrie » Wed, 2020-08-19 06:53
2
1,872 by jlawrie
Thu, 2020-08-20 11:00
Normal topic Fewer than expected structures in clustering output
by fabiotrovato » Thu, 2020-08-20 00:59
0
861 by fabiotrovato
Thu, 2020-08-20 00:59
Normal topic RosettaAntibody3 is failing with "Error: no input sequences were specified!"
by brspurri » Sun, 2020-08-16 16:16
4
2,887 by brspurri
Tue, 2020-08-18 09:57
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
0
810 by fabiotrovato
Mon, 2020-08-17 11:37
Normal topic RosettaCM
by jlawrie » Fri, 2020-08-14 14:09
0
1,556 by jlawrie
Fri, 2020-08-14 14:09
Normal topic mpirun docking_protocol
by NanB » Mon, 2020-08-03 11:38
1
2,948 by ssrb
Fri, 2020-08-14 09:18
Normal topic Docking-I_sc values do not correlate
by jlawrie » Wed, 2020-08-12 08:08
2
1,836 by jlawrie
Wed, 2020-08-12 08:57
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
1,930 by jlawrie
Wed, 2020-08-12 08:56
Normal topic Modeling-Using RosettaCM
by jlawrie » Wed, 2020-08-12 08:46
1
1,163 by jlawrie
Wed, 2020-08-12 08:47
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03
2
1,945 by jlawrie
Wed, 2020-08-12 07:27
Normal topic Error when trying docking protocol with different ligand
by scyphs » Wed, 2020-08-05 04:37
2
1,658 by scyphs
Mon, 2020-08-10 08:09
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
1,631 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic De novo water predictions using SPaDES
by MNP1986 » Mon, 2019-03-25 07:53
1
1,863 by matteoferla
Tue, 2020-08-04 09:30
Normal topic Bug Report - Encoding issue
by daniloboskovic » Tue, 2020-08-04 07:02
0
794 by daniloboskovic
Tue, 2020-08-04 07:02
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
1
1,276 by Andre Serobian
Tue, 2020-07-28 23:26
Normal topic Zero residues error in docking
by cjy318 » Tue, 2020-07-28 19:47
0
1,163 by cjy318
Tue, 2020-07-28 19:47
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
0
1,031 by linhhoang157
Tue, 2020-07-28 12:40
Normal topic clean_pdb not working
by Andre Serobian » Thu, 2020-07-23 04:48
3
2,647 by rmoretti
Tue, 2020-07-28 08:24
Normal topic Comparative modeling of metalloproteins
by ctqwong » Sun, 2020-07-12 13:51
3
2,184 by ctqwong
Mon, 2020-07-27 01:48
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
0
869 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic Translate mover chain X doesnot exist.
by surya » Thu, 2020-07-09 08:36
6
3,525 by rmoretti
Tue, 2020-07-14 10:54
Normal topic Warning: Fold tree is not set properly for density scoring
by ahansel » Mon, 2020-07-13 10:50
1
1,412 by danpf
Tue, 2020-07-14 10:27
Normal topic Problem with mpirun/mpiexec
by ahansel » Fri, 2020-07-10 08:37
1
3,828 by rmoretti
Fri, 2020-07-10 09:59
Normal topic Segmentation Fault during prepacking
by Sunyp_IM » Fri, 2020-06-12 11:24
4
3,403 by Sunyp_IM
Thu, 2020-07-09 18:40
Normal topic Metal Ion in symmetric design
by tschiex » Wed, 2020-07-08 05:28
0
921 by tschiex
Wed, 2020-07-08 05:28
Normal topic PEPSPEC
by Neeraj » Wed, 2018-01-03 02:24
1
1,873 by Andre Serobian
Wed, 2020-07-08 04:44
Normal topic Does antibody_numbering_converter support camelid antibody?
by mxp » Tue, 2020-07-07 01:21
0
923 by mxp
Tue, 2020-07-07 01:21
Normal topic zero standard deviation of I_sc in protein-protein docking
by rohi » Fri, 2020-07-03 22:19
0
873 by rohi
Fri, 2020-07-03 22:20
Normal topic OptimizeMembranePositionMover - This element is not expected
by bjharris » Wed, 2020-07-01 23:21
2
1,996 by bjharris
Thu, 2020-07-02 11:09
Normal topic LoopModeler mover unable to determine cut point
by gszwabowski » Mon, 2020-06-01 13:12
1
1,655 by matteoferla
Thu, 2020-07-02 07:27
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
0
935 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
1,577 by bjharris
Wed, 2020-07-01 23:25
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
0
901 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic "core.kinematics.FoldTree" error upon running RAbD
by Sunyp_IM » Fri, 2020-06-26 17:27
2
1,865 by Sunyp_IM
Fri, 2020-06-26 20:57
Normal topic ligand_docking ligand preparation
by Alison_Yajie » Thu, 2020-05-21 10:21
2
1,709 by Alison_Yajie
Wed, 2020-06-24 12:38
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
0
896 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
2
1,808 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
1
1,258 by ssrb
Mon, 2020-06-22 13:12
Normal topic Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex
by benhardy » Mon, 2020-06-15 09:33
3
2,262 by benhardy
Fri, 2020-06-19 07:55
Normal topic Residue selector
by Alison_Yajie » Wed, 2020-06-17 19:57
0
901 by Alison_Yajie
Thu, 2020-06-18 09:47
Normal topic Constraint generator
by Alison_Yajie » Wed, 2020-06-17 20:14
1
1,235 by Alison_Yajie
Wed, 2020-06-17 20:35
Normal topic metalloprotein ab initio with glutamic acid
by inorgchem » Tue, 2020-06-16 20:45
0
757 by inorgchem
Tue, 2020-06-16 20:45
Normal topic RosettaCM: An internal error has occurred when "Running the Hybridize mover"
by haom » Mon, 2020-06-15 05:56
4
2,573 by haom
Tue, 2020-06-16 05:55
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
1,406 by nannemdp
Sun, 2020-06-07 08:01
Normal topic The usage of antibody_H3.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 22:50
2
2,078 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic "Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-06-04 05:53
0
923 by Sunyp_IM
Thu, 2020-06-04 05:54
Normal topic RosettaAntibodyDesign: How can I run the protocol without allowing design?
by brspurri » Tue, 2020-05-26 08:12
5
3,089 by brspurri
Wed, 2020-06-03 13:20
Normal topic AbinitioRelax detect_disulf_tolerance
by aarono » Tue, 2020-06-02 00:13
0
951 by aarono
Tue, 2020-06-02 00:13
Normal topic ligand_docking_error
by Alison_Yajie » Mon, 2020-04-20 12:27
3
2,345 by YuFei
Sat, 2020-05-30 00:12
Normal topic Problems with mpi version of antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 23:06
0
1,143 by Sunyp_IM
Thu, 2020-05-28 23:07
Normal topic mp_transform optimize with franklin2019 scoring
by benhardy » Thu, 2020-05-28 08:35
0
1,292 by benhardy
Thu, 2020-05-28 08:45
Normal topic What is a rational minimal value for the "-nstruct" option
by Sunyp_IM » Fri, 2020-05-22 01:28
3
2,281 by nannemdp
Sun, 2020-05-24 14:46
Normal topic cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues
by ValentinaSora » Sun, 2020-05-24 12:32
0
1,500 by ValentinaSora
Sun, 2020-05-24 12:32
Normal topic relax and movemap
by Alison_Yajie » Wed, 2020-05-20 21:27
3
2,437 by smlewis
Thu, 2020-05-21 21:05
Normal topic Changing rosetta scoring to favour less hydrophobic areas
by daniloboskovic » Thu, 2020-05-21 03:03
1
1,280 by vmulligan
Thu, 2020-05-21 18:33
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
0
997 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic Modelling temperature dependent RNA structures
by tuleshwori » Tue, 2020-05-19 01:16
2
1,782 by tuleshwori
Thu, 2020-05-21 02:08
Normal topic Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1
by cm21 » Wed, 2020-05-20 08:55
2
1,875 by cm21
Wed, 2020-05-20 11:22
Normal topic Rna Denovo
by helderveras » Wed, 2020-05-06 08:40
5
3,201 by everyday847
Wed, 2020-05-20 08:52
Normal topic Side-chain grafting at the fixed protein and position
by Kazu » Wed, 2020-05-20 08:49
0
856 by Kazu
Wed, 2020-05-20 08:49
Normal topic Transmembrane helix fold-and-dock?
by sarah_b » Tue, 2020-05-12 02:09
3
2,417 by jkleman
Tue, 2020-05-19 15:02
Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
0
941 by Alison_Yajie
Tue, 2020-05-19 08:29
Normal topic RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?
by brspurri » Thu, 2020-05-14 11:15
2
1,721 by brspurri
Thu, 2020-05-14 12:24
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
1,127 by jcampecino
Wed, 2020-05-13 12:22
Normal topic How to run partial_thread in RosettaCM when residure are more than 9999?
by lanselibai » Mon, 2020-05-11 22:43
2
2,311 by lanselibai
Tue, 2020-05-12 20:25
Normal topic How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38
5
3,468 by danpf
Tue, 2020-05-12 10:58
Normal topic Template/Input length mismatch error during RosettaCM
by marinok » Mon, 2020-05-04 13:12
4
2,867 by marinok
Mon, 2020-05-11 12:48
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
0
846 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic Can the Rosetta Antibody Design (RAbD) protocol incorporate glycans?
by ccottrell » Tue, 2020-05-05 20:30
5
3,110 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
1,283 by matteoferla
Mon, 2020-05-04 02:02
Normal topic can remodel add loops in one chain in multichain PDB structure?
by ksteczk » Fri, 2020-05-01 06:26
1
1,498 by matteoferla
Mon, 2020-05-04 01:43
Normal topic BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?
by daniloboskovic » Wed, 2020-04-29 01:17
2
1,872 by daniloboskovic
Wed, 2020-04-29 05:51
Normal topic RosettaDesign error with Option file open failed
by xingqing326 » Sun, 2020-04-19 01:56
4
4,142 by xingqing326
Tue, 2020-04-21 19:11
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
1,460 by ksteczk
Sat, 2020-04-11 11:23
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
1,009 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
1,019 by daniloboskovic
Fri, 2020-04-10 04:24
Normal topic Error with the mpi version of simple_cycpep_predict
by Florent Langenfeld » Wed, 2020-02-05 05:16
5
3,359 by vmulligan
Fri, 2020-04-10 02:54
Normal topic What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001."
by Corvin » Thu, 2020-04-02 00:16
0
1,021 by Corvin
Thu, 2020-04-02 00:16
Normal topic Docking of multichain oligomers
by sdh_h » Wed, 2020-03-25 12:43
0
1,125 by sdh_h
Wed, 2020-03-25 12:43
Normal topic Any progress on getting intermediate structures during a design?
by broomsday » Mon, 2020-03-16 06:46
2
1,981 by vmulligan
Tue, 2020-03-17 11:35
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
0
1,035 by wentlewi
Fri, 2020-03-13 03:24
Normal topic Is native.pdb necess for fragment_picker?
by ylwang » Thu, 2020-03-12 00:57
2
1,980 by ylwang
Thu, 2020-03-12 20:42
Normal topic "sparks failed" error when running "make_fragments.pl"?
by Danielsebas » Tue, 2019-09-03 03:43
6
4,286 by Jacob_Verburgt
Tue, 2020-03-10 14:39
Normal topic score is 0 in the output? - RosettaScripts
by chrisHKL » Thu, 2020-03-05 09:33
0
1,005 by chrisHKL
Thu, 2020-03-05 12:58
Normal topic RosettaScript Segmentation Fault (crash log attached)
by chrisHKL » Thu, 2020-03-05 07:21
2
2,528 by chrisHKL
Thu, 2020-03-05 09:11
Normal topic std::bad_alloc error after changing .xml script?
by chrisHKL » Wed, 2020-03-04 11:44
10
5,859 by jadolfbr
Thu, 2020-03-05 07:02
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
1,800 by chrisHKL
Wed, 2020-03-04 10:49
Normal topic Comparative Modeling Templates for Protein with Multiple Domains
by Morrian_Lynn » Wed, 2020-03-04 10:42
0
915 by Morrian_Lynn
Wed, 2020-03-04 10:42
Normal topic Ddg filter threshold value?
by chrisHKL » Fri, 2020-02-28 15:01
1
1,346 by rmoretti
Wed, 2020-03-04 09:56
Normal topic Imitating induced fit protocol in SymDock2 without any symmetry constraints
by chenna » Fri, 2020-02-14 01:35
2
2,031 by chenna
Wed, 2020-03-04 03:24
Normal topic Filter for fixed-bb design using RosettaScript?
by chrisHKL » Fri, 2020-02-28 19:47
4
2,656 by vmulligan
Mon, 2020-03-02 13:40
Normal topic antibody_numbering_converter cannot recognize the IMGT scheme
by cryosky » Sat, 2020-02-29 23:12
4
3,163 by jadolfbr
Sun, 2020-03-01 14:54
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
1,096 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic remodel ERROR: unrecognized mm_atom_type_name RGU
by daniloboskovic » Sat, 2020-02-22 11:55
1
1,546 by daniloboskovic
Tue, 2020-02-25 08:28
Normal topic Rosetta scripts crash in CM workflow
by jlburkhead » Tue, 2019-12-03 22:55
1
1,695 by danpf
Fri, 2020-02-21 18:37
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