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Rosetta 3 - Applications

Topic / Topic starter Replies Views Last postsort ascending
Normal topic "Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-06-04 05:53
0
391 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
1,462 by brspurri
Wed, 2020-06-03 13:20
Normal topic AbinitioRelax detect_disulf_tolerance
by aarono » Tue, 2020-06-02 00:13
0
518 by aarono
Tue, 2020-06-02 00:13
Normal topic ligand_docking_error
by Alison_Yajie » Mon, 2020-04-20 12:27
3
1,183 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
514 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
585 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
1,071 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
573 by ValentinaSora
Sun, 2020-05-24 12:32
Normal topic relax and movemap
by Alison_Yajie » Wed, 2020-05-20 21:27
3
1,124 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
567 by vmulligan
Thu, 2020-05-21 18:33
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
0
424 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
837 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
858 by cm21
Wed, 2020-05-20 11:22
Normal topic Rna Denovo
by helderveras » Wed, 2020-05-06 08:40
5
1,571 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
358 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
1,163 by jkleman
Tue, 2020-05-19 15:02
Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
0
427 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
797 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
581 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
468 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
1,042 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
1,636 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
1,251 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
385 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
1,416 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
602 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
671 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
868 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
1,713 by xingqing326
Tue, 2020-04-21 19:11
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
648 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
506 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
509 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
1,629 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
526 by Corvin
Thu, 2020-04-02 00:16
Normal topic Docking of multichain oligomers
by sdh_h » Wed, 2020-03-25 12:43
0
568 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
901 by vmulligan
Tue, 2020-03-17 11:35
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
0
519 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
968 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
2,249 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
467 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
1,101 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
2,670 by jadolfbr
Thu, 2020-03-05 07:02
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
857 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
469 by Morrian_Lynn
Wed, 2020-03-04 10:42
Normal topic Ddg filter threshold value?
by chrisHKL » Fri, 2020-02-28 15:01
1
626 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
1,019 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
1,223 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
1,439 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
449 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
682 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
931 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
1,444 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
741 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
631 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
1,852 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
717 by xinmiaohe
Fri, 2020-02-07 13:52
Normal topic error: Unable to open weights/patch file in using ddg_monomer.linuxgccrelease
by xinmiaohe » Thu, 2020-01-30 22:09
1
1,081 by xinmiaohe
Fri, 2020-01-31 08:23
Normal topic Error during single state design
by sujigeorge1979 » Sat, 2020-01-18 00:37
5
2,254 by rmoretti
Thu, 2020-01-30 15:42
Normal topic fixing sequence during grafting in antibody_designer
by COM » Fri, 2020-01-24 11:38
1
743 by jadolfbr
Tue, 2020-01-28 09:13
Normal topic appropriate sampling for protein docking to a multi chain assembly
by SWM » Fri, 2020-01-24 11:22
0
410 by SWM
Fri, 2020-01-24 11:22
Normal topic Limit on backbone movement in relax?
by SWM » Fri, 2020-01-24 07:35
0
499 by SWM
Fri, 2020-01-24 07:35
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
893 by maral.adeli-kou...
Wed, 2020-01-22 12:41
Normal topic Centroid mode minimization
by Martin Floor » Tue, 2020-01-21 07:34
2
986 by Martin Floor
Tue, 2020-01-21 11:15
Normal topic How to freeze ligand during FastRelax?
by dnamkr » Thu, 2020-01-02 14:53
1
873 by aloshbau
Fri, 2020-01-10 16:48
Normal topic cartfrag_overlap error while running hybridize protocol
by sn » Thu, 2017-12-21 10:24
2
1,387 by dnamkr
Mon, 2019-12-30 11:43
Normal topic Can remodel really handle multiple insertions in one simulation?
by lanselibai » Sat, 2019-12-28 12:51
0
465 by lanselibai
Sat, 2019-12-28 12:51
Normal topic Remodel: the pose does not have residue with chain=H, PDBnum=114
by lanselibai » Wed, 2019-12-25 13:35
1
1,003 by lanselibai
Fri, 2019-12-27 09:38
Normal topic RosettaCM hybridize mover error after fragment picking
by amorin » Thu, 2018-09-06 11:03
2
1,457 by dnamkr
Thu, 2019-12-26 10:22
Normal topic Error Implementing Match Style Constraints
by pwging13 » Thu, 2019-12-19 09:53
0
539 by pwging13
Thu, 2019-12-19 09:53
Normal topic using DARC in rosetta
by syntekabio2019 » Thu, 2019-12-12 01:27
0
560 by syntekabio2019
Thu, 2019-12-12 01:27
Normal topic using piper-flexpepdock
by syntekabio2019 » Thu, 2019-12-12 01:22
0
653 by syntekabio2019
Thu, 2019-12-12 01:22
Normal topic Docking the border segments of coiled coils in parallel orientation
by Corvin » Mon, 2019-12-02 02:00
0
527 by Corvin
Mon, 2019-12-02 02:00
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
737 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.
by daniloboskovic » Fri, 2019-11-08 08:24
0
1,330 by daniloboskovic
Fri, 2019-11-08 08:27
Normal topic running in MPI mode and multiple scores per output PDB file?
by dantimatter » Wed, 2019-10-30 09:42
7
2,736 by dantimatter
Wed, 2019-11-06 09:51
Normal topic Alanine Scanning for 1 Protein (no interface)
by mags33 » Fri, 2019-10-25 10:08
2
1,328 by mags33
Wed, 2019-11-06 09:35
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
1,196 by allan.ferrari
Tue, 2019-11-05 16:52
Normal topic Warnings during relax
by cossio » Thu, 2018-10-11 14:42
2
1,778 by rmoretti
Mon, 2019-11-04 13:56
Normal topic Symmetry mode in Remodel for N-terminal extension
by yvonne.chan2 » Mon, 2019-11-04 13:41
0
672 by yvonne.chan2
Mon, 2019-11-04 13:41
Normal topic cryptic error "Got some signal... It is:15" -- an issue with 'fixbb', or something else?
by dantimatter » Wed, 2019-10-16 14:59
5
1,755 by dantimatter
Wed, 2019-10-30 09:43
Normal topic An error with score app
by Genta » Tue, 2019-10-29 18:46
0
630 by Genta
Tue, 2019-10-29 18:46
Normal topic antibody protocol fails
by hamedkhakzad » Mon, 2019-08-19 07:43
1
764 by smlewis
Tue, 2019-10-22 09:45
Normal topic change number of output pose files written out (default=50) in ligand docking XML script
by hdelrisco » Fri, 2019-10-18 13:50
2
940 by hdelrisco
Fri, 2019-10-18 17:16
Normal topic denovo modelling on a virus-coat protein dimer
by aseem121 » Wed, 2019-10-16 06:55
1
786 by danpf
Wed, 2019-10-16 13:03
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
3,524 by Corvin
Tue, 2019-10-15 01:12
Normal topic "install_dependencies.pl" script: an optimization of HDD space during nr-pfilt data extracting and formatting stage
by Corvin » Thu, 2019-10-10 02:20
1
816 by danpf
Thu, 2019-10-10 09:55
Normal topic "Make_fragments.pl" can't connect to dependencies links
by Corvin » Wed, 2019-09-04 23:54
2
1,239 by Corvin
Thu, 2019-10-10 01:12
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
0
501 by CATarr
Wed, 2019-10-09 19:05
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
2,597 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic Energy function and iteration script files
by michelleqyh » Fri, 2019-09-27 09:06
1
679 by smlewis
Fri, 2019-09-27 11:54
Normal topic Structure prediction using true distance and angle constraint
by maruhuang » Wed, 2019-08-21 02:29
4
1,335 by maruhuang
Thu, 2019-09-26 18:52
Normal topic how to "rescore" the models using lowest energy model from rosetta run as native, for RMSD vs Score plot?
by Danielsebas » Tue, 2019-09-24 03:51
1
817 by smlewis
Tue, 2019-09-24 12:43
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
1,685 by smlewis
Mon, 2019-09-23 11:42
Normal topic antibody modeling error
by mxp » Mon, 2019-09-16 18:29
2
1,055 by mxp
Mon, 2019-09-23 01:40
Normal topic Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease
by bdzhh » Tue, 2019-09-17 17:02
1
803 by jadolfbr
Thu, 2019-09-19 08:53
Normal topic Can I use rosetta binaries built in one linux system to another linux system?
by Danielsebas » Wed, 2019-09-18 06:49
1
765 by rmoretti
Wed, 2019-09-18 10:36
Normal topic how to make "static" built binaries use multiple cpus like "mpi"?
by Danielsebas » Wed, 2019-09-18 06:41
3
1,386 by rmoretti
Wed, 2019-09-18 10:21
Normal topic Error with Formatdb of legacy blast when running "install_dependencies.pl"?
by Danielsebas » Mon, 2019-09-16 09:30
2
899 by Danielsebas
Tue, 2019-09-17 01:03
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
741 by smlewis
Mon, 2019-09-16 12:22
Normal topic "Install_dependencies.pl" gives "Aborted" when downloading "nr" database?
by Danielsebas » Sat, 2019-09-14 08:53
3
1,150 by danpf
Mon, 2019-09-16 09:51
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