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Rosetta 3 - Applications

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Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
0
151 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
305 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
206 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
185 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
354 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
581 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
449 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
168 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
523 by jadolfbr
Wed, 2020-05-06 11:37
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
257 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
233 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
306 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
526 by xingqing326
Tue, 2020-04-21 19:11
Normal topic DNA-protein docking
by ksteczk » Sat, 2020-04-11 11:23
0
237 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
229 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
222 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
717 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
221 by Corvin
Thu, 2020-04-02 00:16
Normal topic Docking of multichain oligomers
by sdh_h » Wed, 2020-03-25 12:43
0
275 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
347 by vmulligan
Tue, 2020-03-17 11:35
Normal topic application for affinity optimization
by wentlewi » Fri, 2020-03-13 03:24
0
257 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
404 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
1,114 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
197 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
2,149 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
367 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
967 by jadolfbr
Thu, 2020-03-05 07:02
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
359 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
225 by Morrian_Lynn
Wed, 2020-03-04 10:42
Normal topic Ddg filter threshold value?
by chrisHKL » Fri, 2020-02-28 15:01
1
274 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
413 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
481 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
538 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
195 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
309 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
448 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
672 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
337 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
308 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
1,007 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
297 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
434 by xinmiaohe
Fri, 2020-01-31 08:23
Normal topic Error during single state design
by sujigeorge1979 » Sat, 2020-01-18 00:37
5
742 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
338 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
201 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
254 by SWM
Fri, 2020-01-24 07:35
Normal topic docking with capping groups
by xavierfradera » Sun, 2018-11-04 16:17
1
519 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
395 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
414 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
898 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
240 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
403 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
923 by dnamkr
Thu, 2019-12-26 10:22
Normal topic Error Implementing Match Style Constraints
by pwging13 » Thu, 2019-12-19 09:53
0
289 by pwging13
Thu, 2019-12-19 09:53
Normal topic using DARC in rosetta
by syntekabio2019 » Thu, 2019-12-12 01:27
0
320 by syntekabio2019
Thu, 2019-12-12 01:27
Normal topic using piper-flexpepdock
by syntekabio2019 » Thu, 2019-12-12 01:22
0
341 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
277 by Corvin
Mon, 2019-12-02 02:00
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
386 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
657 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
1,365 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
608 by mags33
Wed, 2019-11-06 09:35
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
553 by allan.ferrari
Tue, 2019-11-05 16:52
Normal topic Warnings during relax
by cossio » Thu, 2018-10-11 14:42
2
949 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
388 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
823 by dantimatter
Wed, 2019-10-30 09:43
Normal topic An error with score app
by Genta » Tue, 2019-10-29 18:46
0
288 by Genta
Tue, 2019-10-29 18:46
Normal topic antibody protocol fails
by hamedkhakzad » Mon, 2019-08-19 07:43
1
382 by smlewis
Tue, 2019-10-22 09:45
Normal topic Speed problem when running RosettaLigand ligand docking
by Nicole Deng » Tue, 2019-10-08 04:29
2
616 by Nicole Deng
Fri, 2019-10-18 19:09
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
434 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
387 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
1,782 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
383 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
612 by Corvin
Thu, 2019-10-10 01:12
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
0
296 by CATarr
Wed, 2019-10-09 19:05
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
1,187 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
352 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
639 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
377 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
829 by smlewis
Mon, 2019-09-23 11:42
Normal topic antibody modeling error
by mxp » Mon, 2019-09-16 18:29
2
538 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
407 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
378 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
682 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
415 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
345 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
569 by danpf
Mon, 2019-09-16 09:51
Normal topic How to make new VALL database?
by Danielsebas » Sun, 2019-09-08 02:16
2
693 by Danielsebas
Wed, 2019-09-11 00:44
Normal topic "make" error in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7"
by Danielsebas » Mon, 2019-09-02 08:14
2
586 by Danielsebas
Sun, 2019-09-08 02:08
Normal topic extract docking pose from ligand docking silent file
by Ruska322 » Sat, 2019-09-07 05:21
0
313 by Ruska322
Sat, 2019-09-07 05:21
Normal topic Unable to understand fragment picking tutorial points.
by Danielsebas » Thu, 2019-09-05 03:44
4
758 by danpf
Fri, 2019-09-06 11:29
Normal topic ligand docking with MPI
by Ruska322 » Wed, 2019-09-04 03:47
2
535 by Ruska322
Fri, 2019-09-06 07:13
Normal topic Rosetta make_fragments.pl error?
by Danielsebas » Mon, 2019-09-02 07:51
3
688 by Danielsebas
Thu, 2019-09-05 03:35
Normal topic /database folder after running "install_dependencies.pl" size 657 GB?
by Danielsebas » Tue, 2019-09-03 03:32
1
333 by danpf
Tue, 2019-09-03 10:15
Normal topic Rosetta fragment tools installation error
by Danielsebas » Thu, 2019-08-29 02:17
2
499 by Danielsebas
Sun, 2019-09-01 02:38
Normal topic how to find help informations on rosetta_scripts in rosetta3.10
by xinmiaohe » Mon, 2019-08-26 14:48
5
813 by xinmiaohe
Tue, 2019-08-27 08:37
Normal topic A problem with "make_fragments.pl" script dependencies
by Corvin » Fri, 2019-08-16 04:30
2
691 by Corvin
Tue, 2019-08-27 00:46
Normal topic can anyone help me correct this script to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:23
1
467 by xinmiaohe
Mon, 2019-08-26 18:16
Normal topic RosettaMatch
by xingqing326 » Mon, 2019-07-22 13:14
1
524 by rmoretti
Mon, 2019-08-26 12:57
Normal topic "Angle constraint: 0-length bonds" error
by purvi24 » Sun, 2019-07-28 10:09
1
440 by rmoretti
Mon, 2019-08-26 12:49
Normal topic PDB file name too long to be handled by file system
by dave » Thu, 2019-08-08 03:10
1
350 by rmoretti
Mon, 2019-08-26 12:17
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