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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
7,938 by admin
Fri, 2015-09-04 16:17
Normal topic Issues with rosetta numbering and keeping ligand when relaxing molecule.
by Wexter300 » Sun, 2024-04-28 14:37
4
324 by Wexter300
Tue, 2024-05-07 10:16
Normal topic Question about computer specifications requirement of RFdiffusion
by ng98 » Mon, 2024-05-06 02:18
1
134 by nannemdp
Mon, 2024-05-06 20:09
Normal topic How do I implement more CPU cores in the execution of FlexPepDock?
by ChoripanSalado » Thu, 2024-05-02 08:55
0
128 by ChoripanSalado
Thu, 2024-05-02 08:55
Normal topic clustering PDBs from docking
by jbujons » Wed, 2024-04-24 08:34
2
127 by jbujons
Wed, 2024-04-24 09:34
Normal topic Discrepancies between Foldit fa_rep score and Rosseta jd2 score fa_rep score
by mrosam » Fri, 2024-04-19 07:57
0
133 by mrosam
Fri, 2024-04-19 07:57
Normal topic Problem with relaxing a PDB around a chemically bound ligand
by drinker615 » Sat, 2024-04-06 16:04
5
369 by drinker615
Tue, 2024-04-16 19:06
Normal topic Scripts and/or strategies for saturation mutagenesis simulations?
by drinker615 » Tue, 2024-04-16 18:43
0
128 by drinker615
Tue, 2024-04-16 18:43
Normal topic Canceling jobs - RosettaDock5.0
by katie » Tue, 2024-04-09 12:30
0
98 by katie
Tue, 2024-04-09 12:30
Normal topic Hamiltonian Exchange
by JSK » Mon, 2024-03-18 12:44
0
171 by JSK
Tue, 2024-03-19 09:21
Normal topic JD3 FastRelax over MPI - crashes on relax completion/before writing output
by aduffy33 » Tue, 2024-03-12 12:51
0
198 by aduffy33
Tue, 2024-03-12 12:52
Normal topic Segmentation Fault
by ileanexis » Mon, 2024-03-11 08:53
0
151 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
1
233 by mdm95
Tue, 2024-03-05 14:05
Normal topic setting timeout option in MPI run
by syntekabio2019 » Mon, 2024-02-26 01:09
5
505 by rmoretti
Wed, 2024-02-28 09:20
Normal topic Global Docking with output analysis RMS
by kwu030 » Fri, 2024-02-23 09:17
1
268 by rmoretti
Mon, 2024-02-26 08:24
Normal topic Rigidifying ligand
by Daniel_Levin » Sun, 2024-02-18 12:10
0
310 by Daniel_Levin
Sun, 2024-02-18 12:10
Normal topic Cartesian_ddG mutfile error
by paulbo » Mon, 2024-02-05 01:25
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399 by paulbo
Mon, 2024-02-05 01:25
Normal topic ddG of multiple mutations on a monomer
by hltorresvera » Mon, 2021-02-01 16:54
1
2,300 by paulbo
Sun, 2024-02-04 22:03
Normal topic [Question] How do the <FILTERS> confidence work?
by jrom » Wed, 2024-01-24 10:25
1
264 by rmoretti
Wed, 2024-01-24 11:55
Normal topic Error about rifdocking
by ng98 » Mon, 2024-01-08 16:21
1
295 by rmoretti
Tue, 2024-01-09 23:41
Normal topic Error when running AqueousPoreFinder protocol
by mluengo » Mon, 2023-12-11 02:55
0
285 by mluengo
Mon, 2023-12-11 03:13
Normal topic FARFAR2 error: [ERROR: Not complementary at positions]
by Eden » Sat, 2023-11-18 02:39
0
253 by Eden
Sat, 2023-11-18 02:39
Normal topic Methodology Feedback with As(III) and Pb(II) Binding
by rnogy » Mon, 2023-11-06 17:05
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277 by rnogy
Mon, 2023-11-06 17:06
Normal topic FARFAR2 Error With Secondary Structure File
by bdh81 » Thu, 2023-11-02 09:01
2
510 by bdh81
Sun, 2023-11-05 16:04
Normal topic protein-protein docking
by LUOD » Thu, 2023-11-02 18:23
0
270 by LUOD
Thu, 2023-11-02 18:25
Normal topic JD3 w/ Silent file output crashing - Option filename not found
by aduffy33 » Mon, 2023-10-30 13:40
2
451 by aduffy33
Mon, 2023-10-30 15:35
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
643 by alove1
Mon, 2023-10-30 13:18
Normal topic Unable to download Rosetta
by Yair Tenorio » Mon, 2023-10-23 11:48
2
487 by Yair Tenorio
Mon, 2023-10-23 12:29
Normal topic Docking antibody to membrane protein
by Yegor_Ko » Thu, 2023-10-12 07:37
2
588 by Yegor_Ko
Fri, 2023-10-20 01:35
Normal topic Problem with sugar parameters
by Martin Floor » Sat, 2023-10-07 10:17
0
496 by Martin Floor
Sat, 2023-10-07 10:17
Normal topic Error in flex ddG tutorial
by wentlewi » Sat, 2020-05-16 08:06
2
1,890 by Alvin Yang
Wed, 2023-10-04 03:34
Normal topic Replacing a single residue in a structure
by Wexter300 » Sat, 2023-09-16 14:23
0
515 by Wexter300
Sat, 2023-09-16 14:23
Normal topic RosettaDock - protonation states
by LWilliamson » Tue, 2023-08-15 08:15
6
1,404 by nannemdp
Thu, 2023-08-24 08:21
Normal topic Predicting conformations of mutated residues
by Delfosse57 » Tue, 2023-08-22 12:26
1
446 by rmoretti
Wed, 2023-08-23 08:26
Normal topic Error when using published constraints file
by Delfosse57 » Thu, 2023-08-17 11:22
2
583 by ikalvet
Mon, 2023-08-21 05:52
Normal topic Generating Params File for water molecule
by Ahmed Raslan » Thu, 2023-08-17 13:13
0
559 by Ahmed Raslan
Thu, 2023-08-17 13:13
Normal topic [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection!
by Jane_002 » Tue, 2023-08-08 21:07
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585 by Jane_002
Tue, 2023-08-08 21:07
Normal topic GALigandDock errors
by Delfosse57 » Mon, 2023-08-07 13:16
0
486 by Delfosse57
Mon, 2023-08-07 13:16
Normal topic different relaxed energy scores for one same protein structure
by ivareve125 » Sun, 2023-07-16 17:54
2
613 by ivareve125
Mon, 2023-07-17 17:37
Normal topic Questions about gen_apo_grids
by JasonIsaac » Sat, 2023-06-17 00:20
0
360 by JasonIsaac
Sat, 2023-06-17 00:20
Normal topic Memory error - double free or corruption
by almeida85 » Thu, 2023-05-25 06:18
0
422 by almeida85
Thu, 2023-05-25 06:18
Normal topic Scoring correlation with electron density map
by mrosam » Thu, 2023-05-25 05:14
0
378 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
0
374 by seamoon
Wed, 2023-05-24 07:46
Normal topic Missing atoms, unable to fill in missing atoms
by kwu030 » Fri, 2023-05-05 12:58
12
4,363 by kwu030
Thu, 2023-05-18 08:31
Normal topic ERROR: beta_nov16(.wts) requested, but -corrections::beta_nov16 not set to true. This leads to a garbage scorefunction.
by sia » Mon, 2023-05-08 06:36
6
1,551 by rmoretti
Tue, 2023-05-16 07:10
Normal topic Figuring out the input flags required for this script
by jjung380 » Wed, 2023-04-19 14:17
3
1,075 by rmoretti
Mon, 2023-05-15 15:23
Normal topic Intel MPI: early exit due to job process stopped.
by jackzzs » Mon, 2023-05-15 02:57
0
1,283 by jackzzs
Mon, 2023-05-15 03:17
Normal topic Calculating SAP score using RosettaScripts
by varunmc99 » Fri, 2023-05-12 11:03
2
907 by varunmc99
Fri, 2023-05-12 11:49
Normal topic Converting all residues to poly-Gly/Ala
by jtpi6174 » Tue, 2023-05-09 14:14
2
721 by jtpi6174
Tue, 2023-05-09 15:51
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42
3
1,993 by rmoretti
Tue, 2023-05-09 15:32
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
0
398 by JasonIsaac
Tue, 2023-05-02 03:39
Normal topic rosie github log in
by YUANXU » Tue, 2023-04-25 20:13
1
541 by Sergey
Thu, 2023-04-27 12:03
Normal topic Any general way to generate .params file for beta and gamma NCAA?
by wwwmrzkwww » Wed, 2023-04-26 12:35
0
407 by wwwmrzkwww
Wed, 2023-04-26 12:35
Normal topic TaskOperations with AntibodyDesignMover
by chenna » Sun, 2023-04-23 23:52
0
382 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
399 by wwwmrzkwww
Sun, 2023-04-23 14:25
Normal topic Error with residue selectors not counting indices correctly.
by Wexter300 » Tue, 2023-04-04 11:04
1
566 by ajasja
Wed, 2023-04-05 00:20
Normal topic Method for adding residues into PDB's w/ RosettaScripts.
by Wexter300 » Wed, 2023-03-15 13:07
1
648 by rmoretti
Thu, 2023-03-16 11:46
Normal topic Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting.
by ldx022 » Thu, 2023-03-09 17:03
3
1,146 by ldx022
Sat, 2023-03-11 16:53
Normal topic RuntimeError: CUDA out of memory.
by ravi.thakkar » Tue, 2023-03-07 00:27
2
855 by rmoretti
Tue, 2023-03-07 08:18
Normal topic Error when trying to use xml script to design PDB
by Wexter300 » Fri, 2023-02-24 13:29
1
676 by rmoretti
Fri, 2023-02-24 13:58
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
0
517 by JasonIsaac
Wed, 2023-02-22 18:36
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
1,755 by rmoretti
Mon, 2023-02-20 16:07
Normal topic can't access rosetta commercial license download via given URL from CoMotion
by y_atsmonraz » Tue, 2023-02-14 11:04
8
1,924 by rmoretti
Thu, 2023-02-16 13:48
Normal topic Rosetta remodelling - how to change the added residue type instead of just VAL
by xuezhi » Wed, 2023-02-15 14:00
0
454 by xuezhi
Wed, 2023-02-15 14:00
Normal topic How to set jump between ligands
by Zehui Zhou » Wed, 2023-02-15 04:48
0
474 by Zehui Zhou
Wed, 2023-02-15 07:12
Normal topic Score function in protein-protein docking with constrains
by Zehui Zhou » Mon, 2023-02-06 03:31
2
1,040 by Zehui Zhou
Wed, 2023-02-15 05:40
Normal topic Truncating a protein using rosetta
by Wexter300 » Mon, 2023-02-13 12:05
2
748 by Wexter300
Mon, 2023-02-13 13:04
Normal topic Segmentation fault with nstruct > 1
by Brian Wiley » Sun, 2023-02-12 20:46
0
449 by Brian Wiley
Sun, 2023-02-12 20:46
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08
4
1,163 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic No values for total score while running Rosetta score file.
by Shweata Maurya » Wed, 2023-02-01 02:05
4
1,249 by Shweata Maurya
Wed, 2023-02-08 03:19
Normal topic Calculating shape complementarity of ligand and protein
by varunmc99 » Tue, 2023-01-17 11:29
1
725 by rmoretti
Mon, 2023-02-06 14:42
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
626 by rmoretti
Mon, 2023-02-06 14:35
Normal topic Error in H3_modeling_scores.fasc file from antibody_H3 program
by Brian Wiley » Sat, 2023-02-04 23:41
0
431 by Brian Wiley
Sat, 2023-02-04 23:43
Normal topic LHOC script problem in Rosetta Antibody
by ziheng@mit.edu » Thu, 2019-04-25 14:19
3
2,349 by Brian Wiley
Sat, 2023-02-04 23:26
Normal topic Run protein-protein docking parallelly by mpi
by Zehui Zhou » Thu, 2023-02-02 06:23
3
1,079 by Zehui Zhou
Fri, 2023-02-03 05:51
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
810 by Brian Wiley
Tue, 2023-01-31 19:08
Normal topic Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi
by SamuelGong » Fri, 2023-01-27 06:20
3
1,024 by rmoretti
Mon, 2023-01-30 08:04
Normal topic Error when attempting to relax pdb, "flag_input_relax" not found
by Wexter300 » Mon, 2023-01-23 11:32
4
1,146 by Wexter300
Wed, 2023-01-25 12:34
Normal topic Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?
by JW_24 » Tue, 2023-01-24 04:40
2
869 by JW_24
Tue, 2023-01-24 14:52
Normal topic Structure Prediction of protein mutant using relax
by Delfosse57 » Tue, 2023-01-10 13:26
1
689 by JW_24
Tue, 2023-01-24 04:55
Normal topic undefined symbol: ZN9CifString12UnknownValueE error meaning?
by aniyaz » Wed, 2023-01-04 08:37
3
1,357 by aniyaz
Wed, 2023-01-11 01:24
Normal topic Different dG_separated from RAbD and InterfaceAnalyzer
by brubin » Mon, 2022-12-19 13:58
2
974 by brubin
Tue, 2022-12-20 13:26
Normal topic Unexpected length of light chain FR1
by mgupta » Fri, 2022-12-09 01:03
0
667 by mgupta
Fri, 2022-12-09 01:03
Normal topic Prepacking crashing using metalloprotein
by mb0261 » Tue, 2022-12-06 10:16
0
606 by mb0261
Tue, 2022-12-06 10:16
Normal topic What should I do to lower down the fa_sol scores?
by JasonIsaac » Mon, 2022-12-05 18:57
0
615 by JasonIsaac
Mon, 2022-12-05 18:57
Normal topic Adding NCAA with Metal Ion
by MustafaBughio » Mon, 2022-11-28 15:07
1
882 by JasonIsaac
Mon, 2022-12-05 18:41
Normal topic Predicting structure of protein after a few mutations
by Delfosse57 » Thu, 2022-12-01 20:40
0
597 by Delfosse57
Thu, 2022-12-01 20:40
Normal topic Loop modeling
by Robertofg » Tue, 2022-11-22 00:34
0
612 by Robertofg
Tue, 2022-11-22 00:34
Normal topic N-Terminal Galactose
by SebastianBB » Mon, 2022-11-21 08:33
0
565 by SebastianBB
Mon, 2022-11-21 08:33
Normal topic Error in rosetta_scripts.mpi.linuxgccrelease: double free or corruption (!prev): 0x0000000007697a90
by almeida85 » Thu, 2022-11-17 01:04
0
591 by almeida85
Thu, 2022-11-17 01:04
Normal topic Where is Sicdock application now? Can I find a substitute?
by JasonIsaac » Sun, 2022-11-13 03:41
3
1,127 by rmoretti
Mon, 2022-11-14 07:27
Normal topic pose.energies().total_enegies().show_nonzero() changes after packer is applied
by Liviu Copoiu » Mon, 2022-11-07 16:51
2
969 by Liviu Copoiu
Tue, 2022-11-08 10:43
Normal topic What is virtual atom means in a params file and how to generate it?
by JasonIsaac » Fri, 2022-11-04 04:53
4
1,649 by JasonIsaac
Mon, 2022-11-07 19:15
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
0
566 by He Xiao
Mon, 2022-11-07 04:10
Normal topic total_score changes when decomposing bb hbonds ref2015
by Liviu Copoiu » Mon, 2022-10-31 15:40
2
913 by Liviu Copoiu
Mon, 2022-10-31 16:03
Normal topic Failure to produce a cst file
by biotech » Wed, 2022-10-26 11:17
0
561 by biotech
Wed, 2022-10-26 11:17
Normal topic On iterations in ddg_monomer
by Proteinmechanic » Fri, 2022-09-30 21:23
0
536 by Proteinmechanic
Fri, 2022-09-30 21:23
Normal topic Save silent results to individual directory by process ID
by Payne » Sat, 2022-09-24 05:23
3
1,166 by rmoretti
Thu, 2022-09-29 00:15
Normal topic Ensemble Docking with RosettaDock 4.0 Protocol
by mb0261 » Wed, 2022-07-27 07:00
1
1,160 by mb0261
Mon, 2022-09-26 07:50
Normal topic GeneralizedKIC side chain closure.
by almeida85 » Mon, 2022-09-19 06:13
0
613 by almeida85
Mon, 2022-09-19 07:22

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