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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
5,801 by admin
Fri, 2015-09-04 16:17
Normal topic Extracting a part of a silent file as another silent file
by almeida85 » Wed, 2021-07-28 23:53
1
46 by zivben
Sat, 2021-07-31 08:16
Normal topic Problem with match on enzdes
by ahuls1 » Thu, 2021-07-29 13:21
1
33 by ahuls1
Thu, 2021-07-29 13:23
Normal topic Better minimization with Rosetta
by Elijah_Hix » Wed, 2021-07-28 13:53
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33 by Elijah_Hix
Wed, 2021-07-28 13:53
Normal topic Scoring in Rosetta
by Elijah_Hix » Wed, 2021-07-14 06:48
1
106 by rmoretti
Wed, 2021-07-14 07:07
Normal topic covalent ligand docking in Rosetta
by rohi » Mon, 2021-06-07 06:39
12
398 by matteoferla
Wed, 2021-07-14 04:03
Normal topic Why does the sum of the per-residue total energy not match the whole score?
by matteoferla » Fri, 2021-07-09 08:36
2
85 by matteoferla
Mon, 2021-07-12 02:23
Normal topic Differences between energy values reported in the tutorials and the ones obtained by running the code, what is normal?
by ericlang » Mon, 2021-07-05 05:43
2
91 by ericlang
Mon, 2021-07-05 06:59
Normal topic Error using ddg_monomer application (Assertion `pose.residue(resnum).name1() == wt` failed)
by sgaray » Thu, 2021-06-24 14:47
2
88 by sgaray
Fri, 2021-06-25 11:26
Normal topic enzyme design and scoring function
by rohi » Fri, 2021-06-25 10:29
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56 by rohi
Fri, 2021-06-25 10:29
Normal topic Add a ligand with only one atom (i.e. Zn) to the RosettaCM
by lanselibai » Tue, 2021-06-22 10:28
6
197 by rmoretti
Thu, 2021-06-24 12:23
Normal topic RosettaCM: threading okay, but hybridize loses many secondary structure
by lanselibai » Wed, 2021-06-23 13:51
2
76 by lanselibai
Thu, 2021-06-24 10:16
Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06
1
54 by lanselibai
Wed, 2021-06-23 14:53
Normal topic RosettaCM: "Ligands must be added to all templates"
by lanselibai » Tue, 2021-06-22 10:42
2
81 by lanselibai
Wed, 2021-06-23 13:21
Normal topic Internal error while running AbinitioRelax
by Subhrodeep Saha » Sun, 2021-06-13 03:44
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125 by rmoretti
Wed, 2021-06-23 02:17
Normal topic adding NCAA to the N-terminal of RCSB pdb
by ate » Tue, 2021-06-08 08:24
4
302 by Subhrodeep Saha
Sat, 2021-06-19 07:17
Normal topic Flex-pep-docking (ab-initio mode)
by ate » Wed, 2021-06-16 19:19
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103 by ate
Wed, 2021-06-16 19:19
Normal topic Obtaining all PDB IDs containing similar binding sites for a specific ligand
by Antonia » Wed, 2021-06-16 12:30
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96 by Antonia
Wed, 2021-06-16 12:30
Normal topic Obtain score during prediction
by CameronJA » Mon, 2021-06-14 16:12
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105 by CameronJA
Mon, 2021-06-14 16:12
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:32
1
125 by taylorjones
Wed, 2021-06-09 16:30
Normal topic parameter file of GLU protonated (GLU_P1.params)
by rohi » Sat, 2021-06-05 20:44
1
130 by nannemdp
Sun, 2021-06-06 09:26
Normal topic Segmentation fault on antibody structure prediction
by dkesar » Fri, 2021-06-04 19:09
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117 by dkesar
Fri, 2021-06-04 19:09
Normal topic FastRelax Mover with symmetry, ligand and membrane
by Michele.Bonus » Wed, 2021-05-26 04:43
1
222 by matteoferla
Thu, 2021-06-03 08:24
Normal topic partial charge of params file in ligand docking
by rohi » Fri, 2021-05-28 08:43
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190 by rmoretti
Fri, 2021-05-28 08:54
Normal topic Meaning of Metalbinding_constraint
by Corvin » Wed, 2021-05-19 07:54
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214 by Corvin
Wed, 2021-05-19 07:54
Normal topic Rosetta Double changing mmCIF chain ID
by Victor Tobiasson » Thu, 2021-05-13 07:57
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271 by Victor Tobiasson
Thu, 2021-05-13 08:33
Normal topic Rotate chain
by Germanico » Sun, 2021-05-09 16:36
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331 by danpf
Mon, 2021-05-10 10:04
Normal topic Calibur not listing cluster members
by Swillard » Sun, 2018-07-01 13:07
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1,123 by benhardy
Fri, 2021-05-07 07:22
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:52
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261 by ate
Sat, 2021-05-01 02:52
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:22
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254 by ate
Sat, 2021-05-01 02:22
Normal topic Speeding up FastDesign
by ebetica0 » Wed, 2021-04-28 13:08
1
233 by vmulligan
Wed, 2021-04-28 14:20
Normal topic Clustering problem
by Suuo » Tue, 2021-04-20 01:40
1
254 by rmoretti
Tue, 2021-04-20 13:06
Normal topic opencl support programs
by x_wuxi » Mon, 2021-04-12 18:17
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254 by rmoretti
Tue, 2021-04-13 06:42
Normal topic ab initio structure modeling
by pci112 » Mon, 2021-04-12 08:07
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227 by pci112
Mon, 2021-04-12 08:12
Normal topic Sequence Profile/Checkpoint file
by ojmel » Fri, 2021-04-02 17:29
1
303 by taylorjones
Mon, 2021-04-05 13:17
Normal topic Ligand being read as part of protein structure
by MarkusAurelius » Thu, 2021-04-01 11:00
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305 by MarkusAurelius
Fri, 2021-04-02 11:44
Normal topic params file for beta-amino acids
by phonez » Mon, 2021-03-29 18:30
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467 by everyday847
Thu, 2021-04-01 11:59
Normal topic clean_pdb.py
by duz » Wed, 2021-03-24 13:36
2
323 by duz
Thu, 2021-04-01 09:34
Normal topic Show I be using beta_nov16 scorefxn?
by matteoferla » Thu, 2021-04-01 04:06
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184 by matteoferla
Thu, 2021-04-01 04:06
Normal topic de novo RNA loop
by c.ocasion » Sun, 2021-02-14 18:34
5
653 by everyday847
Mon, 2021-03-29 20:19
Normal topic Chain name being read as residue
by MarkusAurelius » Mon, 2021-03-22 11:19
2
265 by MarkusAurelius
Mon, 2021-03-29 09:06
Normal topic de novo protein prediction
by pci112 » Tue, 2021-03-23 10:13
2
322 by pci112
Thu, 2021-03-25 01:44
Normal topic MPI optimization on TACC stampede2 HPC
by rlwoltz » Tue, 2021-03-16 18:07
2
342 by rlwoltz
Wed, 2021-03-24 22:36
Normal topic I Need Help on Validation for a Ligand Docking Experiment.
by tbelec » Sat, 2021-03-20 13:27
1
259 by matteoferla
Mon, 2021-03-22 08:29
Normal topic Suppress printing to STDOUT for applications
by tylerborrman » Tue, 2015-11-24 11:37
5
3,276 by code_Monkey
Thu, 2021-03-18 08:03
Normal topic small molecule charge generated by molfile_to_params.py
by rohi » Wed, 2021-03-17 09:35
3
300 by rmoretti
Wed, 2021-03-17 13:52
Normal topic Rosetta and design of ligand binding site
by rohi » Mon, 2021-03-15 06:00
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191 by rohi
Mon, 2021-03-15 06:31
Normal topic Recommendations for CoupledMoves enzyme redesign
by dgm3 » Thu, 2021-03-04 10:53
1
354 by aloshbau
Tue, 2021-03-09 02:47
Normal topic Ab Initio Modelling of Protein with Small-Molecule Cofactor
by jurkm » Thu, 2011-03-10 06:56
14
11,221 by jseco
Mon, 2021-03-08 03:46
Normal topic C-term amidation
by tttt » Tue, 2021-03-02 07:46
2
354 by tttt
Wed, 2021-03-03 09:22
Normal topic Running RosettaScripts, but got an error "src/utility/options/OptionCollection.cc, line 1153, No values of the appropriate type"
by zhoubin » Sun, 2021-02-28 08:51
3
360 by zhoubin
Mon, 2021-03-01 22:11
Normal topic How to export high energy state pdb out of backrub?
by whiteqiu » Mon, 2021-03-01 18:32
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200 by whiteqiu
Mon, 2021-03-01 18:32
Normal topic ERROR: Not complementary at positions
by szcshr123 » Fri, 2021-02-26 05:58
2
361 by szcshr123
Fri, 2021-02-26 14:41
Normal topic Remodel and the depracated EMPTY NC
by matteoferla » Fri, 2021-02-26 07:12
0
200 by matteoferla
Fri, 2021-02-26 07:12
Normal topic Fragment Picker score type weights
by wellsm10 » Mon, 2020-12-14 13:05
1
432 by dgront
Thu, 2021-02-11 08:30
Normal topic multi state protein design
by rohi » Fri, 2020-09-04 08:14
2
680 by rmoretti
Tue, 2021-02-09 13:45
Normal topic running Rosetta with MPI
by rohi » Sat, 2020-09-05 16:06
1
602 by rmoretti
Tue, 2021-02-09 13:44
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12
1
437 by rmoretti
Tue, 2021-02-09 12:35
Normal topic protein design for increasing its affinity towards ligand
by rohi » Fri, 2020-10-30 11:33
1
406 by rmoretti
Tue, 2021-02-09 12:25
Normal topic error running "helix_preassemble_setup.py"
by zahra_AZ » Tue, 2020-11-03 01:54
1
493 by rmoretti
Tue, 2021-02-09 12:19
Normal topic clustering ligand binding mood by ligand RMSD
by rohi » Tue, 2021-01-26 21:11
1
350 by brownbp1
Tue, 2021-02-09 12:12
Normal topic constraint are not imposed during protein-ligand docking
by rohi » Wed, 2020-12-02 11:28
1
404 by rmoretti
Tue, 2021-02-09 12:02
Normal topic Rotamer Library Generation in Rosetta3
by jcminerlanl » Wed, 2016-11-30 07:34
5
3,279 by rmoretti
Tue, 2021-02-09 11:52
Normal topic enzyme design implementation
by rohi » Wed, 2020-12-16 09:54
1
441 by rmoretti
Tue, 2021-02-09 11:30
Normal topic dealing with Large ligand in Ligand docking and enzyme design
by rohi » Mon, 2021-01-04 09:58
1
325 by rmoretti
Tue, 2021-02-09 10:48
Normal topic ddG of multiple mutations on a monomer
by hltorresvera » Mon, 2021-02-01 16:54
0
321 by hltorresvera
Tue, 2021-02-09 10:44
Normal topic Help - Protein-Protein interface design
by Dinesh Kumar » Thu, 2021-01-28 00:47
1
280 by rmoretti
Tue, 2021-02-09 10:29
Normal topic computing Pnear for Rosetta ligand docking
by rohi » Mon, 2021-02-01 08:27
1
320 by rmoretti
Tue, 2021-02-09 09:37
Normal topic Problem with protein and ligand preparation before ligand docking.
by zg148119@ohio.edu » Fri, 2021-02-05 06:47
3
498 by rmoretti
Tue, 2021-02-09 09:22
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39
2
323 by almeida85
Mon, 2021-02-08 09:50
Normal topic Can I compare binding affinity of different ligands using Rosetta?
by zg148119@ohio.edu » Sun, 2020-12-06 11:30
4
1,043 by nannemdp
Fri, 2021-02-05 06:49
Normal topic There is a problem executing “rosetta_scripts.static.linuxgccrelease ”
by zjya » Tue, 2021-02-02 23:44
1
255 by rmoretti
Wed, 2021-02-03 14:45
Normal topic problem plotting results from docking_analyser with provided Rscript
by madammolecular » Mon, 2021-02-01 14:44
0
188 by madammolecular
Mon, 2021-02-01 22:41
Normal topic rna_denovo secstruct_general function
by rvandamme » Mon, 2021-02-01 13:39
0
219 by rvandamme
Mon, 2021-02-01 13:39
Normal topic Issues with angle Constraints during Docking
by LeonhardJS » Thu, 2021-01-28 04:40
2
417 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic contribution of interface residues in binding energy
by rohi » Wed, 2021-01-20 07:33
1
302 by rmoretti
Wed, 2021-01-20 07:39
Normal topic De novo backbone trace from fragments
by Victor Tobiasson » Tue, 2020-12-22 06:34
2
575 by Victor Tobiasson
Tue, 2020-12-22 09:18
Normal topic error in ligand docking
by rohi » Fri, 2020-11-13 10:52
1
584 by rmoretti
Fri, 2020-11-13 12:58
Normal topic Error on rna_denovo_setup.py
by zahra_AZ » Mon, 2020-11-09 02:23
0
412 by zahra_AZ
Mon, 2020-11-09 02:23
Normal topic Chain specific flags
by helenah » Mon, 2020-10-19 03:31
5
1,051 by rmoretti
Fri, 2020-11-06 08:04
Normal topic Problems with Cterm_amidation.txt
by helenah » Thu, 2020-10-08 04:52
8
1,514 by helenah
Tue, 2020-11-03 04:33
Normal topic Comparatively modelled chains are far apart in final structure while the template pdb has all chains in a close-knit complex
by Sunidhi » Sun, 2020-11-01 11:00
0
316 by Sunidhi
Sun, 2020-11-01 11:01
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42
1
445 by rmoretti
Mon, 2020-10-26 19:52
Normal topic Extracting PDBs from a Silent file: "Can't find residue type for ARG"
by avsrivatsa » Sat, 2020-10-17 16:20
2
549 by avsrivatsa
Mon, 2020-10-19 18:16
Normal topic using full atom constraint in docking
by rohi » Thu, 2020-10-15 10:28
0
361 by rohi
Thu, 2020-10-15 10:28
Normal topic Score function: unable to open input_files/1qys.pdb
by Cyrrusm » Tue, 2020-10-13 11:35
1
478 by rmoretti
Tue, 2020-10-13 11:40
Normal topic analyzing the protein protein docking without native structure
by rohi » Sun, 2020-10-11 20:42
2
594 by rohi
Tue, 2020-10-13 09:15
Normal topic loop modelling on complex structure
by Tianyang89 » Fri, 2020-09-18 07:24
1
538 by amelie.stein
Mon, 2020-09-28 10:41
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
6
1,227 by jadolfbr
Thu, 2020-09-24 10:04
Normal topic RosettaRemodel gives no increased output when setting higher -num_trajectory
by JW_24 » Tue, 2020-09-22 11:49
2
600 by JW_24
Wed, 2020-09-23 01:27
Normal topic Error with simple_cycpep_predict protocol while using a native pdb file
by Florent Langenfeld » Tue, 2019-03-26 10:05
3
1,113 by Florent Langenfeld
Tue, 2020-09-22 03:03
Normal topic CryoEM model refinement with covalent conjugated prosthetic Phosphopantetheine carrying acyl group
by ZhijunW » Thu, 2020-09-03 18:36
11
2,063 by matteoferla
Sat, 2020-09-12 03:02
Normal topic 4mer 6mer fragment database
by bjharris » Wed, 2020-09-09 15:12
2
691 by bjharris
Wed, 2020-09-09 20:04
Normal topic RosettaCM: help to generate similar models as those from Robetta Server
by haom » Wed, 2020-09-09 09:19
0
390 by haom
Wed, 2020-09-09 09:19
Normal topic what factors determine the lowest (best) LigInterfaceEnergy score?
by jmaly » Wed, 2020-08-26 13:07
0
432 by jmaly
Wed, 2020-09-02 16:16
Normal topic How RosettaCM can perform part of C terminal domain (CTD) structure prediction without proper template structures (coordinates)
by haom » Tue, 2020-09-01 13:21
0
368 by haom
Tue, 2020-09-01 18:50
Normal topic RosettaCM: adding constraints while keeping AUTO constraints
by Michele.Bonus » Sun, 2020-08-30 10:42
2
675 by Michele.Bonus
Sun, 2020-08-30 23:06
Normal topic Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.
by nferruz » Fri, 2020-08-28 06:04
0
413 by nferruz
Fri, 2020-08-28 06:05
Normal topic Compile C++ Rosetta to Pyrosetta ERROR
by michelleqyh » Fri, 2020-08-21 09:00
0
339 by michelleqyh
Fri, 2020-08-21 09:00
Normal topic DockingProtocol mover ensemble error
by dfcoelho » Tue, 2018-10-16 08:32
2
1,345 by brspurri
Thu, 2020-08-20 13:22

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