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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
7,880 by admin
Fri, 2015-09-04 16:17
Normal topic Hamiltonian Exchange
by JSK » Mon, 2024-03-18 12:44
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71 by JSK
Tue, 2024-03-19 09:21
Normal topic Segmentation Fault
by ileanexis » Mon, 2024-03-11 08:53
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77 by ileanexis
Mon, 2024-03-11 08:53
Normal topic Filters saying atom type does not exist on residue
by mdm95 » Mon, 2024-03-04 15:13
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101 by mdm95
Tue, 2024-03-05 14:05
Normal topic JD3 FastRelax over MPI - crashes on relax completion/before writing output
by aduffy33 » Tue, 2024-03-12 12:51
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106 by aduffy33
Tue, 2024-03-12 12:52
Normal topic Global Docking with output analysis RMS
by kwu030 » Fri, 2024-02-23 09:17
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161 by rmoretti
Mon, 2024-02-26 08:24
Normal topic [Question] How do the <FILTERS> confidence work?
by jrom » Wed, 2024-01-24 10:25
1
177 by rmoretti
Wed, 2024-01-24 11:55
Normal topic Error about rifdocking
by ng98 » Mon, 2024-01-08 16:21
1
204 by rmoretti
Tue, 2024-01-09 23:41
Normal topic FARFAR2 error: [ERROR: Not complementary at positions]
by Eden » Sat, 2023-11-18 02:39
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206 by Eden
Sat, 2023-11-18 02:39
Normal topic protein-protein docking
by LUOD » Thu, 2023-11-02 18:23
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216 by LUOD
Thu, 2023-11-02 18:25
Normal topic Methodology Feedback with As(III) and Pb(II) Binding
by rnogy » Mon, 2023-11-06 17:05
0
220 by rnogy
Mon, 2023-11-06 17:06
Normal topic Error when running AqueousPoreFinder protocol
by mluengo » Mon, 2023-12-11 02:55
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230 by mluengo
Mon, 2023-12-11 03:13
Normal topic Rigidifying ligand
by Daniel_Levin » Sun, 2024-02-18 12:10
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243 by Daniel_Levin
Sun, 2024-02-18 12:10
Normal topic setting timeout option in MPI run
by syntekabio2019 » Mon, 2024-02-26 01:09
5
247 by rmoretti
Wed, 2024-02-28 09:20
Normal topic Questions about gen_apo_grids
by JasonIsaac » Sat, 2023-06-17 00:20
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304 by JasonIsaac
Sat, 2023-06-17 00:20
Normal topic Cartesian_ddG mutfile error
by paulbo » Mon, 2024-02-05 01:25
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319 by paulbo
Mon, 2024-02-05 01:25
Normal topic Scoring correlation with electron density map
by mrosam » Thu, 2023-05-25 05:14
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325 by mrosam
Thu, 2023-05-25 05:14
Normal topic Changing amino acid profile while keeping the backbone conformation between 2 protein structures (need help)
by seamoon » Wed, 2023-05-24 07:46
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325 by seamoon
Wed, 2023-05-24 07:46
Normal topic TaskOperations with AntibodyDesignMover
by chenna » Sun, 2023-04-23 23:52
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332 by chenna
Sun, 2023-04-23 23:52
Normal topic how to generate _prepro.rama file for a customized beta-amino acid residues?
by wwwmrzkwww » Sun, 2023-04-23 14:25
0
339 by wwwmrzkwww
Sun, 2023-04-23 14:25
Normal topic How many rifdock can I run at a time on a 64 CPUs and 512GB memory server?
by JasonIsaac » Tue, 2023-05-02 03:39
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340 by JasonIsaac
Tue, 2023-05-02 03:39
Normal topic JD3 w/ Silent file output crashing - Option filename not found
by aduffy33 » Mon, 2023-10-30 13:40
2
355 by aduffy33
Mon, 2023-10-30 15:35
Normal topic Any general way to generate .params file for beta and gamma NCAA?
by wwwmrzkwww » Wed, 2023-04-26 12:35
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356 by wwwmrzkwww
Wed, 2023-04-26 12:35
Normal topic Memory error - double free or corruption
by almeida85 » Thu, 2023-05-25 06:18
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368 by almeida85
Thu, 2023-05-25 06:18
Normal topic Predicting conformations of mutated residues
by Delfosse57 » Tue, 2023-08-22 12:26
1
369 by rmoretti
Wed, 2023-08-23 08:26
Normal topic FARFAR2 Error With Secondary Structure File
by bdh81 » Thu, 2023-11-02 09:01
2
373 by bdh81
Sun, 2023-11-05 16:04
Normal topic Unable to download Rosetta
by Yair Tenorio » Mon, 2023-10-23 11:48
2
380 by Yair Tenorio
Mon, 2023-10-23 12:29
Normal topic Error in H3_modeling_scores.fasc file from antibody_H3 program
by Brian Wiley » Sat, 2023-02-04 23:41
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381 by Brian Wiley
Sat, 2023-02-04 23:43
Normal topic Rosetta remodelling - how to change the added residue type instead of just VAL
by xuezhi » Wed, 2023-02-15 14:00
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388 by xuezhi
Wed, 2023-02-15 14:00
Normal topic Segmentation fault with nstruct > 1
by Brian Wiley » Sun, 2023-02-12 20:46
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404 by Brian Wiley
Sun, 2023-02-12 20:46
Normal topic How to set jump between ligands
by Zehui Zhou » Wed, 2023-02-15 04:48
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420 by Zehui Zhou
Wed, 2023-02-15 07:12
Normal topic GALigandDock errors
by Delfosse57 » Mon, 2023-08-07 13:16
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430 by Delfosse57
Mon, 2023-08-07 13:16
Normal topic Problem with sugar parameters
by Martin Floor » Sat, 2023-10-07 10:17
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432 by Martin Floor
Sat, 2023-10-07 10:17
Normal topic Temperature
by mrosam » Mon, 2022-08-08 01:37
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462 by mrosam
Mon, 2022-08-08 01:37
Normal topic Docking antibody to membrane protein
by Yegor_Ko » Thu, 2023-10-12 07:37
2
462 by Yegor_Ko
Fri, 2023-10-20 01:35
Normal topic rosie github log in
by YUANXU » Tue, 2023-04-25 20:13
1
466 by Sergey
Thu, 2023-04-27 12:03
Normal topic Which application/mover should I use to evaluate the ddg between apo enzyme and enzyme binding with transition state?
by JasonIsaac » Wed, 2023-02-22 18:36
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469 by JasonIsaac
Wed, 2023-02-22 18:36
Normal topic Replacing a single residue in a structure
by Wexter300 » Sat, 2023-09-16 14:23
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469 by Wexter300
Sat, 2023-09-16 14:23
Normal topic Interface scores comparison
by NingNing » Tue, 2022-08-09 17:36
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477 by NingNing
Tue, 2022-08-09 17:36
Normal topic Error with residue selectors not counting indices correctly.
by Wexter300 » Tue, 2023-04-04 11:04
1
479 by ajasja
Wed, 2023-04-05 00:20
Normal topic How to add new Movers to Rosetta
by mb0261 » Thu, 2022-06-30 10:48
0
482 by mb0261
Thu, 2022-06-30 10:48
Normal topic RosettaDock-3.2 output
by Zjq1998 » Wed, 2022-06-15 23:54
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483 by Zjq1998
Wed, 2022-06-15 23:54
Normal topic protein location change during Docking protocol
by Hyun » Tue, 2022-03-29 19:53
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484 by Hyun
Tue, 2022-03-29 19:53
Normal topic Error when using published constraints file
by Delfosse57 » Thu, 2023-08-17 11:22
2
486 by ikalvet
Mon, 2023-08-21 05:52
Normal topic On iterations in ddg_monomer
by Proteinmechanic » Fri, 2022-09-30 21:23
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492 by Proteinmechanic
Fri, 2022-09-30 21:23
Normal topic Antigen-antibody modeling
by aastha.pal » Mon, 2022-06-27 09:34
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496 by aastha.pal
Mon, 2022-06-27 09:34
Normal topic Rosettascript - change residue number and chain ID
by cttm4a1 » Wed, 2022-09-14 23:40
0
498 by cttm4a1
Wed, 2022-09-14 23:40
Normal topic Problems with ICOOR when generating polymer params file
by liuwenxi » Tue, 2022-08-09 08:33
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501 by liuwenxi
Tue, 2022-08-09 08:33
Normal topic Generating Params File for water molecule
by Ahmed Raslan » Thu, 2023-08-17 13:13
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501 by Ahmed Raslan
Thu, 2023-08-17 13:13
Normal topic Failure to produce a cst file
by biotech » Wed, 2022-10-26 11:17
0
505 by biotech
Wed, 2022-10-26 11:17
Normal topic Proper indexing of grafted residues by CCDEndsGraftMover
by cttm4a1 » Wed, 2022-09-07 23:41
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506 by cttm4a1
Wed, 2022-09-07 23:41
Normal topic N-Terminal Galactose
by SebastianBB » Mon, 2022-11-21 08:33
0
508 by SebastianBB
Mon, 2022-11-21 08:33
Normal topic ERROR: Assertion `build_sets_[ build_set_id ].restype().has( "1HA" )` failed. ERROR:: Exit from: src/protocols/match/upstream/Pr
by alove1 » Sat, 2023-10-28 17:19
3
508 by alove1
Mon, 2023-10-30 13:18
Normal topic Error with sequence_tolerance.R processing the checkpoint files, *.ga.entities and *.ga.generations.
by He Xiao » Mon, 2022-11-07 03:41
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510 by He Xiao
Mon, 2022-11-07 04:10
Normal topic Ensemble file required for both partners with docking prepack protocol
by katherinemccoy » Tue, 2022-03-29 14:26
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513 by katherinemccoy
Tue, 2022-03-29 14:26
Normal topic Porblem with Rosetta Homology Modelling
by Karthik » Wed, 2022-07-13 23:45
0
514 by Karthik
Wed, 2022-07-13 23:45
Normal topic Get fasta from PDB script correction - Solved
by ialvy » Tue, 2022-08-30 00:00
0
517 by ialvy
Tue, 2022-08-30 00:00
Normal topic Error in rosetta_scripts.mpi.linuxgccrelease: double free or corruption (!prev): 0x0000000007697a90
by almeida85 » Thu, 2022-11-17 01:04
0
518 by almeida85
Thu, 2022-11-17 01:04
Normal topic different relaxed energy scores for one same protein structure
by ivareve125 » Sun, 2023-07-16 17:54
2
520 by ivareve125
Mon, 2023-07-17 17:37
Normal topic [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection!
by Jane_002 » Tue, 2023-08-08 21:07
0
521 by Jane_002
Tue, 2023-08-08 21:07
Normal topic Question about remodelling
by tonycheng1688 » Mon, 2022-04-25 13:51
0
523 by tonycheng1688
Mon, 2022-04-25 13:51
Normal topic Predicting structure of protein after a few mutations
by Delfosse57 » Thu, 2022-12-01 20:40
0
544 by Delfosse57
Thu, 2022-12-01 20:40
Normal topic Loop modeling
by Robertofg » Tue, 2022-11-22 00:34
0
555 by Robertofg
Tue, 2022-11-22 00:34
Normal topic What should I do to lower down the fa_sol scores?
by JasonIsaac » Mon, 2022-12-05 18:57
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557 by JasonIsaac
Mon, 2022-12-05 18:57
Normal topic Designing Feasible Backbones
by csvajda » Sat, 2022-08-13 08:08
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557 by csvajda
Sat, 2022-08-13 08:08
Normal topic Prepacking crashing using metalloprotein
by mb0261 » Tue, 2022-12-06 10:16
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558 by mb0261
Tue, 2022-12-06 10:16
Normal topic Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.
by SubhaK » Thu, 2023-01-26 21:29
1
562 by rmoretti
Mon, 2023-02-06 14:35
Normal topic rosetta scripts to superimpose multiple segments
by rlwoltz » Fri, 2022-04-29 15:15
0
562 by rlwoltz
Fri, 2022-04-29 15:15
Normal topic GeneralizedKIC side chain closure.
by almeida85 » Mon, 2022-09-19 06:13
0
563 by almeida85
Mon, 2022-09-19 07:22
Normal topic Method for adding residues into PDB's w/ RosettaScripts.
by Wexter300 » Wed, 2023-03-15 13:07
1
584 by rmoretti
Thu, 2023-03-16 11:46
Normal topic Converting all residues to poly-Gly/Ala
by jtpi6174 » Tue, 2023-05-09 14:14
2
603 by jtpi6174
Tue, 2023-05-09 15:51
Normal topic Error when trying to use xml script to design PDB
by Wexter300 » Fri, 2023-02-24 13:29
1
606 by rmoretti
Fri, 2023-02-24 13:58
Normal topic Structure Prediction of protein mutant using relax
by Delfosse57 » Tue, 2023-01-10 13:26
1
611 by JW_24
Tue, 2023-01-24 04:55
Normal topic Unexpected length of light chain FR1
by mgupta » Fri, 2022-12-09 01:03
0
613 by mgupta
Fri, 2022-12-09 01:03
Normal topic Design strategy - One chain at a time OR two chains together?
by tlopes » Wed, 2022-01-05 18:19
0
621 by tlopes
Wed, 2022-01-05 18:19
Normal topic Calculating shape complementarity of ligand and protein
by varunmc99 » Tue, 2023-01-17 11:29
1
645 by rmoretti
Mon, 2023-02-06 14:42
Normal topic SnugDock or RosettaDock for HDX-MS data
by hanzhiz » Thu, 2021-12-16 09:18
0
649 by hanzhiz
Thu, 2021-12-16 09:18
Normal topic Help with file in article Kemp elimination catalysts by computational enzyme design
by Wenithor » Sat, 2021-10-09 07:23
0
657 by Wenithor
Sat, 2021-10-09 07:23
Normal topic protein binder interface design error
by guowuchen » Thu, 2022-06-23 04:43
0
658 by guowuchen
Thu, 2022-06-23 04:43
Normal topic Error when using rna_denovo in TACC stampede2 HPC
by lsong2 » Thu, 2021-11-18 10:31
0
659 by lsong2
Thu, 2021-11-18 10:31
Normal topic Truncating a protein using rosetta
by Wexter300 » Mon, 2023-02-13 12:05
2
660 by Wexter300
Mon, 2023-02-13 13:04
Normal topic core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP
by to-qinbin@163.com » Wed, 2022-09-14 06:06
1
665 by rmoretti
Wed, 2022-09-14 09:14
Normal topic mpi_MSD for antibody design
by hanzhiz » Thu, 2021-12-16 09:32
0
677 by hanzhiz
Thu, 2021-12-16 09:32
Normal topic Sequence symmetry during FastDesign for repeat protein design
by cttm4a1 » Tue, 2022-09-06 21:02
1
685 by rmoretti
Wed, 2022-09-07 09:19
Normal topic mol2genparams.py script dependencies
by dhirajks » Wed, 2022-06-08 16:46
1
692 by matteoferla
Thu, 2022-06-09 14:41
Normal topic Unrecognized D-Leu name / C-terminal ACE
by almeida85 » Thu, 2022-08-11 07:43
1
692 by almeida85
Fri, 2022-08-12 05:56
Normal topic RMSD filter
by Soler » Sat, 2022-01-15 22:09
0
704 by Soler
Sat, 2022-01-15 22:09
Normal topic Obtaining all PDB IDs containing similar binding sites for a specific ligand
by Antonia » Wed, 2021-06-16 12:30
0
715 by Antonia
Wed, 2021-06-16 12:30
Normal topic Multiple Relax runnings
by mb0261 » Sat, 2022-08-27 05:42
1
716 by rmoretti
Tue, 2022-09-06 08:22
Normal topic Should all input structures to energy_based_clustering have an output pdb file?
by Brian Wiley » Mon, 2023-01-30 20:42
2
716 by Brian Wiley
Tue, 2023-01-31 19:08
Normal topic Global ligand docking with Rosetta script and PyRosetta
by tisozaki » Tue, 2021-12-14 17:16
0
717 by tisozaki
Tue, 2021-12-14 17:16
Normal topic Generate template parameter file for a polymer
by anarob » Fri, 2022-06-10 11:05
1
718 by matteoferla
Fri, 2022-06-17 10:38
Normal topic SecundaryStructure Filter
by Soler » Sat, 2021-11-20 23:41
0
720 by Soler
Sat, 2021-11-20 23:41
Normal topic Obtain score during prediction
by CameronJA » Mon, 2021-06-14 16:12
0
720 by CameronJA
Mon, 2021-06-14 16:12
Normal topic Flex-pep-docking (ab-initio mode)
by ate » Wed, 2021-06-16 19:19
0
731 by ate
Wed, 2021-06-16 19:19
Normal topic Using specific rotamers
by sahn97 » Fri, 2022-08-26 13:45
1
731 by rmoretti
Fri, 2022-08-26 14:51
Normal topic enzyme design and scoring function
by rohi » Fri, 2021-06-25 10:29
0
740 by rohi
Fri, 2021-06-25 10:29
Normal topic Calculating SAP score using RosettaScripts
by varunmc99 » Fri, 2023-05-12 11:03
2
743 by varunmc99
Fri, 2023-05-12 11:49
Normal topic RuntimeError: CUDA out of memory.
by ravi.thakkar » Tue, 2023-03-07 00:27
2
748 by rmoretti
Tue, 2023-03-07 08:18
Normal topic ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)
by Ken » Mon, 2022-05-23 07:16
1
748 by ajasja
Mon, 2022-05-23 07:19

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