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Rosetta 3 - Applications

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Normal topic RosettaCM
by jlawrie » Fri, 2020-08-14 14:09
0
367 by jlawrie
Fri, 2020-08-14 14:09
Normal topic mpirun docking_protocol
by NanB » Mon, 2020-08-03 11:38
1
568 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
455 by jlawrie
Wed, 2020-08-12 08:57
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
482 by jlawrie
Wed, 2020-08-12 08:56
Normal topic Modeling-Using RosettaCM
by jlawrie » Wed, 2020-08-12 08:46
1
299 by jlawrie
Wed, 2020-08-12 08:47
Normal topic Docking-RMS value nan
by jlawrie » Wed, 2020-08-12 07:03
2
457 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
469 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
437 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
738 by matteoferla
Tue, 2020-08-04 09:30
Normal topic Bug Report - Encoding issue
by daniloboskovic » Tue, 2020-08-04 07:02
0
187 by daniloboskovic
Tue, 2020-08-04 07:02
Normal topic pepspec anchor dock
by Andre Serobian » Tue, 2020-07-28 05:51
1
355 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
245 by cjy318
Tue, 2020-07-28 19:47
Normal topic RosettaAntibody3 core.pose.util error
by linhhoang157 » Tue, 2020-07-28 12:40
0
303 by linhhoang157
Tue, 2020-07-28 12:40
Normal topic clean_pdb not working
by Andre Serobian » Thu, 2020-07-23 04:48
3
667 by rmoretti
Tue, 2020-07-28 08:24
Normal topic Comparative modeling of metalloproteins
by ctqwong » Sun, 2020-07-12 13:51
3
643 by ctqwong
Mon, 2020-07-27 01:48
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
5
896 by jadolfbr
Fri, 2020-07-24 07:24
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
0
246 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
1,059 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
376 by danpf
Tue, 2020-07-14 10:27
Normal topic Problem with mpirun/mpiexec
by ahansel » Fri, 2020-07-10 08:37
1
721 by rmoretti
Fri, 2020-07-10 09:59
Normal topic Segmentation Fault during prepacking
by Sunyp_IM » Fri, 2020-06-12 11:24
4
879 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
267 by tschiex
Wed, 2020-07-08 05:28
Normal topic PEPSPEC
by Neeraj » Wed, 2018-01-03 02:24
1
845 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
228 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
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254 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
550 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
446 by matteoferla
Thu, 2020-07-02 07:27
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
0
256 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
590 by bjharris
Wed, 2020-07-01 23:25
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
0
250 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic Noncanonical amino acids
by wsgosal » Tue, 2014-03-18 05:29
5
3,764 by Nolanm15
Tue, 2020-06-30 08:43
Normal topic "core.kinematics.FoldTree" error upon running RAbD
by Sunyp_IM » Fri, 2020-06-26 17:27
2
541 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
549 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
250 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
540 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
336 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
629 by benhardy
Fri, 2020-06-19 07:55
Normal topic Residue selector
by Alison_Yajie » Wed, 2020-06-17 19:57
0
271 by Alison_Yajie
Thu, 2020-06-18 09:47
Normal topic Constraint generator
by Alison_Yajie » Wed, 2020-06-17 20:14
1
372 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
213 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
690 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
423 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
604 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
251 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
853 by brspurri
Wed, 2020-06-03 13:20
Normal topic AbinitioRelax detect_disulf_tolerance
by aarono » Tue, 2020-06-02 00:13
0
324 by aarono
Tue, 2020-06-02 00:13
Normal topic ligand_docking_error
by Alison_Yajie » Mon, 2020-04-20 12:27
3
820 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
339 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
382 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
699 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
369 by ValentinaSora
Sun, 2020-05-24 12:32
Normal topic relax and movemap
by Alison_Yajie » Wed, 2020-05-20 21:27
3
708 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
379 by vmulligan
Thu, 2020-05-21 18:33
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
0
283 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
520 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
541 by cm21
Wed, 2020-05-20 11:22
Normal topic Rna Denovo
by helderveras » Wed, 2020-05-06 08:40
5
1,005 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
237 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
751 by jkleman
Tue, 2020-05-19 15:02
Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
0
264 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
514 by brspurri
Thu, 2020-05-14 12:24
Normal topic Multistate design issues with -run:msd_job_dist option and MSDMover
by elaine.thai » Wed, 2020-05-13 18:07
0
335 by elaine.thai
Wed, 2020-05-13 18:07
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
303 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
633 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
996 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
807 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
269 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
916 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
395 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
438 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
542 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
954 by xingqing326
Tue, 2020-04-21 19:11
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
392 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
345 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
353 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
1,084 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
344 by Corvin
Thu, 2020-04-02 00:16
Normal topic Docking of multichain oligomers
by sdh_h » Wed, 2020-03-25 12:43
0
391 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
567 by vmulligan
Tue, 2020-03-17 11:35
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
0
373 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
643 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
1,605 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
298 by chrisHKL
Thu, 2020-03-05 12:58
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
4
2,662 by Morrian_Lynn
Thu, 2020-03-05 10:07
Normal topic RosettaScript Segmentation Fault (crash log attached)
by chrisHKL » Thu, 2020-03-05 07:21
2
637 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
1,672 by jadolfbr
Thu, 2020-03-05 07:02
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
571 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
329 by Morrian_Lynn
Wed, 2020-03-04 10:42
Normal topic Ddg filter threshold value?
by chrisHKL » Fri, 2020-02-28 15:01
1
430 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
644 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
778 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
870 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
300 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
451 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
686 by danpf
Fri, 2020-02-21 18:37
Normal topic Options "-out:prefix" didn't work
by maruhuang » Tue, 2019-09-10 05:42
4
995 by danpf
Fri, 2020-02-21 18:32
Normal topic Protein-Protein Docking or Comparative Modeling
by Morrian_Lynn » Wed, 2020-01-29 19:01
1
483 by danpf
Fri, 2020-02-21 18:23
Normal topic How can I model ligands in comparative modeling
by Morrian_Lynn » Thu, 2020-02-20 09:57
1
444 by danpf
Fri, 2020-02-21 17:05
Normal topic Docking to TM protein plus lipid bilayer
by renedominik » Tue, 2019-03-12 06:58
3
1,393 by renedominik
Tue, 2020-02-18 01:36
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
484 by xinmiaohe
Fri, 2020-02-07 13:52
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