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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
6,173 by admin
Fri, 2015-09-04 16:17
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
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14 by smlewis
Wed, 2021-09-22 13:12
Normal topic Rosetta Enzyme design cst block raises error
by cryosky » Thu, 2021-09-16 08:47
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66 by cryosky
Fri, 2021-09-17 22:04
Normal topic pmut and scoring
by ldlamini » Tue, 2021-09-14 00:46
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103 by matteoferla
Mon, 2021-09-20 06:05
Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06
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135 by lanselibai
Wed, 2021-06-23 14:53
Normal topic enzyme design and scoring function
by rohi » Fri, 2021-06-25 10:29
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142 by rohi
Fri, 2021-06-25 10:29
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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152 by Antonia
Wed, 2021-06-16 12:30
Normal topic Flex-pep-docking (ab-initio mode)
by ate » Wed, 2021-06-16 19:19
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155 by ate
Wed, 2021-06-16 19:19
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
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166 by patcD
Wed, 2021-09-01 06:54
Normal topic Obtain score during prediction
by CameronJA » Mon, 2021-06-14 16:12
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169 by CameronJA
Mon, 2021-06-14 16:12
Normal topic RosettaCM: threading okay, but hybridize loses many secondary structure
by lanselibai » Wed, 2021-06-23 13:51
2
173 by lanselibai
Thu, 2021-06-24 10:16
Normal topic RosettaCM: "Ligands must be added to all templates"
by lanselibai » Tue, 2021-06-22 10:42
2
174 by lanselibai
Wed, 2021-06-23 13:21
Normal topic Segmentation fault on antibody structure prediction
by dkesar » Fri, 2021-06-04 19:09
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185 by dkesar
Fri, 2021-06-04 19:09
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
186 by ericlang
Mon, 2021-07-05 06:59
Normal topic parameter file of GLU protonated (GLU_P1.params)
by rohi » Sat, 2021-06-05 20:44
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196 by nannemdp
Sun, 2021-06-06 09:26
Normal topic Internal error while running AbinitioRelax
by Subhrodeep Saha » Sun, 2021-06-13 03:44
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197 by rmoretti
Wed, 2021-06-23 02:17
Normal topic How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion
by wwwmrzkwww » Sun, 2021-08-15 00:19
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200 by wwwmrzkwww
Sun, 2021-08-15 00:19
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:32
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200 by taylorjones
Wed, 2021-06-09 16:30
Normal topic Error using ddg_monomer application (Assertion `pose.residue(resnum).name1() == wt` failed)
by sgaray » Thu, 2021-06-24 14:47
2
205 by sgaray
Fri, 2021-06-25 11:26
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
209 by matteoferla
Mon, 2021-07-12 02:23
Normal topic the question about ddg of disulfide bond mutants
by asbelx » Sun, 2021-08-29 06:40
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212 by asbelx
Wed, 2021-09-08 23:19
Normal topic Explicit water
by tsztain » Wed, 2021-08-25 05:54
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221 by matteoferla
Thu, 2021-09-02 03:50
Normal topic problem plotting results from docking_analyser with provided Rscript
by madammolecular » Mon, 2021-02-01 14:44
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240 by madammolecular
Mon, 2021-02-01 22:41
Normal topic How to export high energy state pdb out of backrub?
by whiteqiu » Mon, 2021-03-01 18:32
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246 by whiteqiu
Mon, 2021-03-01 18:32
Normal topic calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)
by rlwoltz » Tue, 2021-08-03 23:26
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246 by rlwoltz
Tue, 2021-08-03 23:26
Normal topic Rosetta and design of ligand binding site
by rohi » Mon, 2021-03-15 06:00
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251 by rohi
Mon, 2021-03-15 06:31
Normal topic Problem with match on enzdes
by ahuls1 » Thu, 2021-07-29 13:21
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261 by ahuls1
Thu, 2021-07-29 13:23
Normal topic Scoring in Rosetta
by Elijah_Hix » Wed, 2021-07-14 06:48
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264 by rmoretti
Wed, 2021-07-14 07:07
Normal topic Remodel and the depracated EMPTY NC
by matteoferla » Fri, 2021-02-26 07:12
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266 by matteoferla
Fri, 2021-02-26 07:12
Normal topic Meaning of Metalbinding_constraint
by Corvin » Wed, 2021-05-19 07:54
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266 by Corvin
Wed, 2021-05-19 07:54
Normal topic Show I be using beta_nov16 scorefxn?
by matteoferla » Thu, 2021-04-01 04:06
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266 by matteoferla
Thu, 2021-04-01 04:06
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09
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267 by matteoferla
Fri, 2021-08-20 08:37
Normal topic partial charge of params file in ligand docking
by rohi » Fri, 2021-05-28 08:43
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269 by rmoretti
Fri, 2021-05-28 08:54
Normal topic rna_denovo secstruct_general function
by rvandamme » Mon, 2021-02-01 13:39
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274 by rvandamme
Mon, 2021-02-01 13:39
Normal topic ab initio structure modeling
by pci112 » Mon, 2021-04-12 08:07
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285 by pci112
Mon, 2021-04-12 08:12
Normal topic Extracting a part of a silent file as another silent file
by almeida85 » Wed, 2021-07-28 23:53
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293 by zivben
Sat, 2021-07-31 08:16
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:22
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301 by ate
Sat, 2021-05-01 02:22
Normal topic Better minimization with Rosetta
by Elijah_Hix » Wed, 2021-07-28 13:53
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305 by matteoferla
Mon, 2021-08-09 01:53
Normal topic FastRelax Mover with symmetry, ligand and membrane
by Michele.Bonus » Wed, 2021-05-26 04:43
1
308 by matteoferla
Thu, 2021-06-03 08:24
Normal topic Speeding up FastDesign
by ebetica0 » Wed, 2021-04-28 13:08
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315 by vmulligan
Wed, 2021-04-28 14:20
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:52
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322 by ate
Sat, 2021-05-01 02:52
Normal topic opencl support programs
by x_wuxi » Mon, 2021-04-12 18:17
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323 by rmoretti
Tue, 2021-04-13 06:42
Normal topic There is a problem executing “rosetta_scripts.static.linuxgccrelease ”
by zjya » Tue, 2021-02-02 23:44
1
324 by rmoretti
Wed, 2021-02-03 14:45
Normal topic I Need Help on Validation for a Ligand Docking Experiment.
by tbelec » Sat, 2021-03-20 13:27
1
329 by matteoferla
Mon, 2021-03-22 08:29
Normal topic Clustering problem
by Suuo » Tue, 2021-04-20 01:40
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332 by rmoretti
Tue, 2021-04-20 13:06
Normal topic Rosetta Double changing mmCIF chain ID
by Victor Tobiasson » Thu, 2021-05-13 07:57
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346 by Victor Tobiasson
Thu, 2021-05-13 08:33
Normal topic Add a ligand with only one atom (i.e. Zn) to the RosettaCM
by lanselibai » Tue, 2021-06-22 10:28
6
346 by rmoretti
Thu, 2021-06-24 12:23
Normal topic Chain name being read as residue
by MarkusAurelius » Mon, 2021-03-22 11:19
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353 by MarkusAurelius
Mon, 2021-03-29 09:06
Normal topic Quick mysql output question
by pedro.guillem » Thu, 2020-07-23 03:45
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353 by pedro.guillem
Thu, 2020-07-23 03:45
Normal topic Help - Protein-Protein interface design
by Dinesh Kumar » Thu, 2021-01-28 00:47
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359 by rmoretti
Tue, 2021-02-09 10:29
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
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364 by Sunidhi
Sun, 2020-11-01 11:01
Normal topic Sequence Profile/Checkpoint file
by ojmel » Fri, 2021-04-02 17:29
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369 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
2
371 by MarkusAurelius
Fri, 2021-04-02 11:44
Normal topic Compile C++ Rosetta to Pyrosetta ERROR
by michelleqyh » Fri, 2020-08-21 09:00
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376 by michelleqyh
Fri, 2020-08-21 09:00
Normal topic I made a params file generation webpage
by matteoferla » Wed, 2020-07-22 03:08
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379 by matteoferla
Wed, 2020-07-22 03:08
Normal topic contribution of interface residues in binding energy
by rohi » Wed, 2021-01-20 07:33
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380 by rmoretti
Wed, 2021-01-20 07:39
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
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383 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic Make fragments
by jeanramos » Mon, 2020-07-13 00:56
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383 by jeanramos
Mon, 2020-07-13 00:56
Normal topic Output "per-residue" energy score to database
by pedro.guillem » Thu, 2020-05-14 04:22
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389 by pedro.guillem
Thu, 2020-05-14 04:22
Normal topic Finding affinity-reducing mutants towards a ligand in Ligand-based interface design protocol
by adityapadhi » Wed, 2020-06-24 01:29
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391 by adityapadhi
Wed, 2020-06-24 01:29
Normal topic dealing with Large ligand in Ligand docking and enzyme design
by rohi » Mon, 2021-01-04 09:58
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392 by rmoretti
Tue, 2021-02-09 10:48
Normal topic BUG REPORT: MySql column protocol.protocol_id must have the AUTO_INCREMENT flag set
by pedro.guillem » Wed, 2020-05-13 18:31
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399 by pedro.guillem
Wed, 2020-06-24 04:42
Normal topic Clustering error - Help, please
by karolcia1010 » Wed, 2020-06-17 11:19
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399 by karolcia1010
Wed, 2020-06-17 11:19
Normal topic computing Pnear for Rosetta ligand docking
by rohi » Mon, 2021-02-01 08:27
1
402 by rmoretti
Tue, 2021-02-09 09:37
Normal topic "Rosetta predictions of density, heat of vaporization (∆Hvap) and heat capacity (Cp(l))"
by matteoferla » Tue, 2020-07-14 01:51
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402 by matteoferla
Tue, 2020-07-14 01:51
Normal topic small molecule charge generated by molfile_to_params.py
by rohi » Wed, 2021-03-17 09:35
3
403 by rmoretti
Wed, 2021-03-17 13:52
Normal topic Error with filter in rosseta_scripts
by Osmany Guirola » Mon, 2020-05-11 04:52
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410 by Osmany Guirola
Mon, 2020-05-11 04:52
Normal topic using full atom constraint in docking
by rohi » Thu, 2020-10-15 10:28
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412 by rohi
Thu, 2020-10-15 10:28
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
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413 by haom
Tue, 2020-09-01 18:50
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39
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413 by almeida85
Mon, 2021-02-08 09:50
Normal topic clean_pdb.py
by duz » Wed, 2021-03-24 13:36
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419 by duz
Thu, 2021-04-01 09:34
Normal topic de novo protein prediction
by pci112 » Tue, 2021-03-23 10:13
2
419 by pci112
Thu, 2021-03-25 01:44
Normal topic Questions about alanine scanning in Rosetta
by LTJ » Mon, 2020-07-06 14:13
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421 by LTJ
Mon, 2020-07-06 14:13
Normal topic Recommendations for CoupledMoves enzyme redesign
by dgm3 » Thu, 2021-03-04 10:53
1
424 by aloshbau
Tue, 2021-03-09 02:47
Normal topic Structure refinement for helical assembles using Rosetta
by xiaoyanzi » Thu, 2020-06-18 00:34
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429 by xiaoyanzi
Thu, 2020-06-18 00:36
Normal topic Unrecognized atom parameter with denovo_density
by kalabharath » Mon, 2020-06-29 06:59
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429 by kalabharath
Mon, 2020-06-29 06:59
Normal topic Does it make sense to perform Docking on a complex?
by chrisHKL » Mon, 2020-02-17 09:12
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429 by chrisHKL
Mon, 2020-02-17 09:12
Normal topic C-term amidation
by tttt » Tue, 2021-03-02 07:46
2
430 by tttt
Wed, 2021-03-03 09:22
Normal topic Rotate chain
by Germanico » Sun, 2021-05-09 16:36
3
431 by danpf
Mon, 2021-05-10 10:04
Normal topic ligand docking error
by YuFei » Wed, 2020-04-22 17:27
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431 by YuFei
Wed, 2020-04-22 17:27
Normal topic clustering ligand binding mood by ligand RMSD
by rohi » Tue, 2021-01-26 21:11
1
437 by brownbp1
Tue, 2021-02-09 12:12
Normal topic adding NCAA to the N-terminal of RCSB pdb
by ate » Tue, 2021-06-08 08:24
4
439 by Subhrodeep Saha
Sat, 2021-06-19 07:17
Normal topic ddG of multiple mutations on a monomer
by hltorresvera » Mon, 2021-02-01 16:54
0
441 by hltorresvera
Tue, 2021-02-09 10:44
Normal topic RosettaCM: help to generate similar models as those from Robetta Server
by haom » Wed, 2020-09-09 09:19
0
442 by haom
Wed, 2020-09-09 09:19
Normal topic Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.
by nferruz » Fri, 2020-08-28 06:04
0
451 by nferruz
Fri, 2020-08-28 06:05
Normal topic ERROR: Not complementary at positions
by szcshr123 » Fri, 2021-02-26 05:58
2
451 by szcshr123
Fri, 2021-02-26 14:41
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
456 by zhoubin
Mon, 2021-03-01 22:11
Normal topic MPI optimization on TACC stampede2 HPC
by rlwoltz » Tue, 2021-03-16 18:07
2
459 by rlwoltz
Wed, 2021-03-24 22:36
Normal topic Side-chain grafting in fixed scaffold
by Kazu » Wed, 2020-05-20 08:45
0
461 by Kazu
Wed, 2020-05-20 11:58
Normal topic Error on rna_denovo_setup.py
by zahra_AZ » Mon, 2020-11-09 02:23
0
465 by zahra_AZ
Mon, 2020-11-09 02:23
Normal topic protein design for increasing its affinity towards ligand
by rohi » Fri, 2020-10-30 11:33
1
479 by rmoretti
Tue, 2021-02-09 12:25
Normal topic what factors determine the lowest (best) LigInterfaceEnergy score?
by jmaly » Wed, 2020-08-26 13:07
0
490 by jmaly
Wed, 2020-09-02 16:16
Normal topic constraint are not imposed during protein-ligand docking
by rohi » Wed, 2020-12-02 11:28
1
492 by rmoretti
Tue, 2021-02-09 12:02
Normal topic Searching density map using real space correlation
by ahmadkhalifa » Fri, 2018-12-28 00:28
0
496 by ahmadkhalifa
Fri, 2018-12-28 00:28
Normal topic Fragment Picker score type weights
by wellsm10 » Mon, 2020-12-14 13:05
1
497 by dgront
Thu, 2021-02-11 08:30
Normal topic how to perform model quality assessment of rosetta generated models?
by Danielsebas » Tue, 2019-09-24 05:03
0
498 by Danielsebas
Tue, 2019-09-24 05:03
Normal topic Issues with angle Constraints during Docking
by LeonhardJS » Thu, 2021-01-28 04:40
2
498 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic Correct way to force a specific histidine tautomer
by matteoferla » Fri, 2020-04-10 02:40
0
498 by matteoferla
Fri, 2020-04-10 02:40
Normal topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:17
0
509 by yinasun
Fri, 2019-07-26 02:17
Normal topic SARS-CoV-2: call for compound predictions against protease
by matteoferla » Sun, 2020-03-22 05:29
0
510 by matteoferla
Sun, 2020-03-22 05:29

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