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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
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5,445 by admin
Fri, 2015-09-04 16:17
Normal topic protein design for increasing its affinity towards ligand
by rohi » Fri, 2020-10-30 11:33
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16 by rohi
Fri, 2020-10-30 11:33
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42
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41 by rmoretti
Mon, 2020-10-26 19:52
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12
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45 by wentlewi
Sat, 2020-10-24 10:12
Normal topic using full atom constraint in docking
by rohi » Thu, 2020-10-15 10:28
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68 by rohi
Thu, 2020-10-15 10:28
Normal topic Chain specific flags
by helenah » Mon, 2020-10-19 03:31
1
77 by rmoretti
Mon, 2020-10-19 07:23
Normal topic Score function: unable to open input_files/1qys.pdb
by Cyrrusm » Tue, 2020-10-13 11:35
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88 by rmoretti
Tue, 2020-10-13 11:40
Normal topic Extracting PDBs from a Silent file: "Can't find residue type for ARG"
by avsrivatsa » Sat, 2020-10-17 16:20
2
107 by avsrivatsa
Mon, 2020-10-19 18:16
Normal topic Compile C++ Rosetta to Pyrosetta ERROR
by michelleqyh » Fri, 2020-08-21 09:00
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116 by michelleqyh
Fri, 2020-08-21 09:00
Normal topic Quick mysql output question
by pedro.guillem » Thu, 2020-07-23 03:45
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116 by pedro.guillem
Thu, 2020-07-23 03:45
Normal topic I made a params file generation webpage
by matteoferla » Wed, 2020-07-22 03:08
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125 by matteoferla
Wed, 2020-07-22 03:08
Normal topic analyzing the protein protein docking without native structure
by rohi » Sun, 2020-10-11 20:42
2
125 by rohi
Tue, 2020-10-13 09:15
Normal topic RosettaCM: help to generate similar models as those from Robetta Server
by haom » Wed, 2020-09-09 09:19
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128 by haom
Wed, 2020-09-09 09:19
Normal topic Clustering error - Help, please
by karolcia1010 » Wed, 2020-06-17 11:19
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135 by karolcia1010
Wed, 2020-06-17 11:19
Normal topic Questions about alanine scanning in Rosetta
by LTJ » Mon, 2020-07-06 14:13
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139 by LTJ
Mon, 2020-07-06 14:13
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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140 by matteoferla
Tue, 2020-07-14 01:51
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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146 by haom
Tue, 2020-09-01 18:50
Normal topic Make fragments
by jeanramos » Mon, 2020-07-13 00:56
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146 by jeanramos
Mon, 2020-07-13 00:56
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
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148 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic Unrecognized atom parameter with denovo_density
by kalabharath » Mon, 2020-06-29 06:59
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148 by kalabharath
Mon, 2020-06-29 06:59
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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156 by adityapadhi
Wed, 2020-06-24 01:29
Normal topic Structure refinement for helical assembles using Rosetta
by xiaoyanzi » Thu, 2020-06-18 00:34
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158 by xiaoyanzi
Thu, 2020-06-18 00:36
Normal topic reading of AtomPair failed in relax with constraint
by hajar » Wed, 2020-06-10 10:02
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163 by hajar
Wed, 2020-06-10 11:17
Normal topic Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.
by nferruz » Fri, 2020-08-28 06:04
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167 by nferruz
Fri, 2020-08-28 06:05
Normal topic Gaussian Constraint For Dihedrals
by jinli711 » Thu, 2020-07-23 10:47
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171 by matteoferla
Fri, 2020-07-24 03:06
Normal topic what factors determine the lowest (best) LigInterfaceEnergy score?
by jmaly » Wed, 2020-08-26 13:07
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179 by jmaly
Wed, 2020-09-02 16:16
Normal topic Error with filter in rosseta_scripts
by Osmany Guirola » Mon, 2020-05-11 04:52
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182 by Osmany Guirola
Mon, 2020-05-11 04:52
Normal topic Output "per-residue" energy score to database
by pedro.guillem » Thu, 2020-05-14 04:22
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182 by pedro.guillem
Thu, 2020-05-14 04:22
Normal topic RosettaRemodel gives no increased output when setting higher -num_trajectory
by JW_24 » Tue, 2020-09-22 11:49
2
183 by JW_24
Wed, 2020-09-23 01:27
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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185 by pedro.guillem
Wed, 2020-06-24 04:42
Normal topic error when using script best_ifaceE.py
by windmill » Thu, 2020-06-18 21:30
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186 by windmill
Thu, 2020-06-18 21:32
Normal topic Correct way to force a specific histidine tautomer
by matteoferla » Fri, 2020-04-10 02:40
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188 by matteoferla
Fri, 2020-04-10 02:40
Normal topic Side-chain grafting in fixed scaffold
by Kazu » Wed, 2020-05-20 08:45
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188 by Kazu
Wed, 2020-05-20 11:58
Normal topic ligand docking error
by YuFei » Wed, 2020-04-22 17:27
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198 by YuFei
Wed, 2020-04-22 17:27
Normal topic loop modelling on complex structure
by Tianyang89 » Fri, 2020-09-18 07:24
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202 by amelie.stein
Mon, 2020-09-28 10:41
Normal topic Problems with Cterm_amidation.txt
by helenah » Thu, 2020-10-08 04:52
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203 by matteoferla
Thu, 2020-10-22 01:27
Normal topic simple_cycpep_predict issue modifying terminal residue
by JEaston » Thu, 2020-06-25 13:15
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206 by vmulligan
Mon, 2020-06-29 13:09
Normal topic Ligand docking: how to generate the crystal_complex.pdb with hydrogens added
by nhinguyen26 » Wed, 2020-06-17 15:03
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209 by matteoferla
Sat, 2020-06-20 03:56
Normal topic Difference between interface_delta_X and dG_separated?
by Nicole Deng » Sat, 2020-06-06 06:31
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210 by Nicole Deng
Sat, 2020-06-06 06:40
Normal topic RosettaCM: adding constraints while keeping AUTO constraints
by Michele.Bonus » Sun, 2020-08-30 10:42
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211 by Michele.Bonus
Sun, 2020-08-30 23:06
Normal topic multi state protein design
by rohi » Fri, 2020-09-04 08:14
1
219 by smlewis
Fri, 2020-09-04 11:25
Normal topic Controlling Input in the Tutorial
by Smbat » Wed, 2020-07-29 22:41
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220 by Smbat
Thu, 2020-07-30 03:07
Normal topic patch file modification for ser_phosphorylated.txt
by hajar » Sun, 2020-06-21 00:49
1
222 by matteoferla
Tue, 2020-06-23 10:58
Normal topic Error when trying to thread target sequence over template pdbs, partial_thread.static.macosclangrelease not working properly
by DGR95 » Wed, 2020-04-15 14:42
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223 by DGR95
Fri, 2020-04-17 11:25
Normal topic Does it make sense to perform Docking on a complex?
by chrisHKL » Mon, 2020-02-17 09:12
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224 by chrisHKL
Mon, 2020-02-17 09:12
Normal topic running Rosetta with MPI
by rohi » Sat, 2020-09-05 16:06
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225 by rohi
Mon, 2020-09-07 15:24
Normal topic 4mer 6mer fragment database
by bjharris » Wed, 2020-09-09 15:12
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227 by bjharris
Wed, 2020-09-09 20:04
Normal topic str::out_of_range with mpiexec and relax
by pedro.guillem » Fri, 2020-06-19 10:39
1
235 by pedro.guillem
Wed, 2020-06-24 04:49
Normal topic where is PyIgClassfiy.py ?
by mxp » Tue, 2020-07-07 23:57
2
241 by mxp
Wed, 2020-07-08 23:25
Normal topic Error in flex ddG tutorial
by wentlewi » Sat, 2020-05-16 08:06
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254 by wentlewi
Sat, 2020-05-16 08:06
Normal topic Setting output values using a database (with relax app)
by pedro.guillem » Thu, 2020-05-14 04:33
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264 by pedro.guillem
Wed, 2020-06-24 04:41
Normal topic Rosetta changing Atom Name in PDB ATOM record?
by chrisHKL » Tue, 2020-03-03 20:50
1
278 by smlewis
Wed, 2020-03-04 07:40
Normal topic Program frozen at "protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1"
by Xinhang » Sat, 2020-04-11 14:30
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282 by vmulligan
Sat, 2020-04-11 17:40
Normal topic Docking Metalloprotein-Protein
by fgomes » Fri, 2019-11-22 19:12
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282 by fgomes
Fri, 2019-11-22 19:12
Normal topic SARS-CoV-2: call for compound predictions against protease
by matteoferla » Sun, 2020-03-22 05:29
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290 by matteoferla
Sun, 2020-03-22 05:29
Normal topic Protein Interface Design using PSSM
by ccruz » Sun, 2020-05-24 14:27
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294 by nannemdp
Tue, 2020-05-26 06:33
Normal topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:17
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300 by yinasun
Fri, 2019-07-26 02:17
Normal topic I made a RDKit Chem.Mol to params converter — feedback welcome!
by matteoferla » Sun, 2020-05-03 10:14
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303 by jadolfbr
Sun, 2020-05-03 19:38
Normal topic Are 100 structures the maximum generated when using homology_with_end_extension (broker protocol)?
by thaisarns » Fri, 2020-02-21 05:46
1
305 by sheehajh
Fri, 2020-02-21 12:41
Normal topic Method for WebServer Fragment Generation
by Jacob_Verburgt » Tue, 2020-06-02 07:29
2
307 by Jacob_Verburgt
Tue, 2020-06-02 10:26
Normal topic Error in molfile_to_params_polymer.py for NCAA
by kkuo33 » Mon, 2020-05-18 16:41
1
310 by matteoferla
Sat, 2020-05-23 03:09
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
6
312 by jadolfbr
Thu, 2020-09-24 10:04
Normal topic Is there other online server for generate fragment?
by ylwang » Wed, 2020-04-01 01:39
1
314 by rmoretti
Wed, 2020-04-01 10:10
Normal topic how to perform model quality assessment of rosetta generated models?
by Danielsebas » Tue, 2019-09-24 05:03
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320 by Danielsebas
Tue, 2019-09-24 05:03
Normal topic use_truncated_termini not working in combination with params files
by georg » Thu, 2020-03-26 13:14
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327 by matteoferla
Tue, 2020-04-14 03:36
Normal topic error in mol2 to params conversion for GAliganddocking
by jalan » Wed, 2020-04-22 06:08
2
328 by jalan
Thu, 2020-04-23 05:19
Normal topic Searching density map using real space correlation
by ahmadkhalifa » Fri, 2018-12-28 00:28
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339 by ahmadkhalifa
Fri, 2018-12-28 00:28
Normal topic Error in src/protocols/membrane/util.cc line: 1224
by renedominik » Tue, 2020-02-11 08:10
1
340 by renedominik
Wed, 2020-02-12 06:16
Normal topic mpi + mp_mutate_relax
by decrSTL » Thu, 2020-01-16 10:47
1
347 by jkleman
Thu, 2020-01-16 11:05
Normal topic What is the best protocol to predict the missing residues in X-ray crystallisation?
by lanselibai » Sun, 2019-12-29 04:44
1
350 by matteoferla
Wed, 2020-01-01 04:30
Normal topic MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"
by dfcoelho » Mon, 2020-02-03 11:09
1
352 by dfcoelho
Tue, 2020-02-04 07:45
Normal topic Working through tutorials: expected output scorces differ from calculated results
by j.schmue » Sat, 2020-01-18 13:16
2
364 by j.schmue
Tue, 2020-01-28 13:31
Normal topic Disulfidize mover
by karenjgonzalez » Wed, 2019-07-31 12:35
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369 by karenjgonzalez
Wed, 2019-07-31 12:35
Normal topic How to define the surface (???.surf) for surface_docking?
by Anpu » Thu, 2018-09-27 07:34
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377 by Anpu
Thu, 2018-09-27 23:36
Normal topic I got so many atoms in one residue
by ylwang » Tue, 2020-03-24 04:40
3
378 by ylwang
Tue, 2020-03-24 19:35
Normal topic selecting pivot_residue in Backrub for ensemble generation
by rohi » Fri, 2020-08-07 15:41
6
383 by matteoferla
Tue, 2020-08-11 10:00
Normal topic How to use the <CavityVolume> filter in the released version of Rosetta
by BioPython » Sun, 2019-05-12 20:07
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386 by BioPython
Sun, 2019-05-12 20:07
Normal topic Error in Hybridize of Rosetta Comparative Modeling.
by Ivan » Fri, 2019-11-01 07:46
1
400 by rmoretti
Mon, 2019-11-04 12:54
Normal topic Ddg calculation for a metalloprotein using APBS
by dfcoelho » Tue, 2019-11-19 10:06
2
405 by dfcoelho
Wed, 2019-11-20 05:39
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
405 by rmoretti
Tue, 2019-07-09 15:59
Normal topic Denovo density excess map input and segmentation
by ahmadkhalifa » Mon, 2018-04-30 07:28
0
406 by ahmadkhalifa
Fri, 2018-05-04 07:50
Normal topic How to specify constraints during fold-and-dock?
by sarah_b » Tue, 2020-05-12 01:55
3
407 by matteoferla
Thu, 2020-05-14 07:01
Normal topic crashed when loading RDC data
by yangshen12 » Fri, 2018-10-26 12:34
0
413 by yangshen12
Fri, 2018-10-26 12:34
Normal topic AbinitioRelax of RCSB PDB structures
by ac.research » Tue, 2019-09-03 02:35
1
416 by danpf
Tue, 2019-09-03 10:39
Normal topic Ligand question - aromatic bonds not being enforced?
by Rick_Baker » Wed, 2019-09-11 09:08
1
417 by Rick_Baker
Wed, 2019-09-11 15:35
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53
0
420 by ela
Fri, 2018-08-31 02:53
Normal topic MakeRotLib
by yinasun » Sun, 2019-07-28 20:08
1
420 by rmoretti
Mon, 2019-08-26 15:00
Normal topic Unable to create col_complex.pdb file
by sayan500 » Tue, 2019-07-30 22:08
1
425 by rmoretti
Mon, 2019-08-26 14:52
Normal topic restrict PackRotamersMover
by pmit » Thu, 2018-05-03 01:48
0
426 by pmit
Thu, 2018-05-03 01:48
Normal topic Errors in Interface_design_demo
by zhoubin » Fri, 2019-01-04 13:14
0
426 by zhoubin
Fri, 2019-01-04 13:14
Normal topic env energy term
by bazzoli » Wed, 2018-10-10 01:59
0
429 by bazzoli
Wed, 2018-10-10 01:59
Normal topic alignblast.pl truncated file
by rlwoltz » Mon, 2019-03-11 18:32
0
432 by rlwoltz
Mon, 2019-03-11 18:32
Normal topic How to get fragment library from robetta server for mre than 1000 residue sequence?
by Danielsebas » Wed, 2019-09-18 07:53
1
436 by rmoretti
Wed, 2019-09-18 10:49
Normal topic Job Distribution Error
by ac.research » Mon, 2020-02-10 08:22
2
437 by ac.research
Fri, 2020-02-14 23:33
Normal topic Mutations are ignored (fixbb) when using -auto_setup_metals option
by hdelrisco » Wed, 2019-06-19 15:43
1
439 by smlewis
Fri, 2019-06-28 13:56
Normal topic File specification of binary part of silent file (especially PDB section)
by m.ebert » Wed, 2019-05-29 01:52
1
440 by smlewis
Wed, 2019-05-29 13:21
Normal topic IS there any source code about protein structure prediction with only sequences information?
by ylwang » Mon, 2019-07-08 02:36
1
441 by rmoretti
Mon, 2019-07-08 08:05
Normal topic FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py
by obdulia » Wed, 2018-04-18 00:45
0
444 by obdulia
Wed, 2018-04-18 00:45
Normal topic Mutate multidomain protein
by frankfurter1 » Wed, 2018-05-09 04:40
0
450 by frankfurter1
Wed, 2018-05-09 04:40
Normal topic Rosetta Resfile header
by G Mustafa » Mon, 2020-01-20 06:45
2
450 by G Mustafa
Tue, 2020-01-21 06:04

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