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Rosetta 3 - General

Topic / Topic startersort descending Replies Views Last post
Normal topic flexible backbone design (fixbb+relax)
by sdh_h » Mon, 2013-02-04 03:19
9
12,081 by gsmurphy
Mon, 2014-04-21 06:47
Normal topic Flexible backbone design using PSSM
by kalicuta » Thu, 2012-07-26 13:38
4
5,068 by rmoretti
Mon, 2014-04-21 06:47
Normal topic FlexPepDocking.mpi.linuxgccrelease bails out ERROR: total_residue() != 0 ERROR:: Exit from: src/core/pose/Pose.cc line: 1369
by knutjbj » Thu, 2011-02-03 03:24
2
4,531 by knutjbj
Mon, 2014-04-21 06:47
Normal topic Fluctuations in I_sc
by eminegenetics » Thu, 2018-09-13 12:07
4
3,285 by eminegenetics
Fri, 2018-09-21 07:42
Normal topic Fold tree error
by mansi » Tue, 2010-05-18 07:43
2
3,967 by mansi
Mon, 2014-04-21 06:47
Normal topic force field, energy function
by masterofpuppets » Wed, 2015-01-21 11:06
3
6,177 by masterofpuppets
Tue, 2015-01-27 07:07
Normal topic force hydrogen rebuild on input
by jtmacd » Mon, 2013-11-18 08:28
2
3,079 by jtmacd
Mon, 2014-04-21 06:48
Normal topic force point mutation with fixbb
by Anonymous » Wed, 2012-06-13 09:15
3
4,017 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fragment file viewers
by MajorID » Fri, 2012-02-24 20:57
2
2,813 by smlewis
Mon, 2014-04-21 06:47
Normal topic Fragment files
by exchhattu » Fri, 2009-09-18 01:04
4
4,738 by rmoretti
Tue, 2015-01-06 09:58
Normal topic Fragment picker
by phanvy » Mon, 2014-12-08 04:25
2
3,324 by phanvy
Wed, 2014-12-10 00:17
Normal topic Fragment Picker score type weights
by wellsm10 » Mon, 2020-12-14 13:05
1
1,487 by dgront
Thu, 2021-02-11 08:30
Normal topic fragment picking with 100% sequence identity
by nawsad » Thu, 2013-12-05 07:12
1
3,107 by rmoretti
Mon, 2014-04-21 06:48
Normal topic fragment-based loop modeling to get a helix at the loop site
by berk » Wed, 2013-05-29 06:00
11
10,459 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Fragments for short peptides using Robetta
by renedominik » Wed, 2018-05-16 14:21
3
2,964 by renedominik
Mon, 2018-06-04 00:04
Normal topic fragment_picker error secondarysimilarity.cc line:132
by leanawen » Mon, 2013-04-15 14:33
1
2,179 by smlewis
Mon, 2014-04-21 06:47
Normal topic fragment_picker problem
by adva » Tue, 2012-12-18 01:15
13
12,784 by sabine
Mon, 2014-04-21 06:47
Normal topic Free FSC score for validating refinement
by ahmadkhalifa » Thu, 2018-05-10 05:53
2
2,489 by ahmadkhalifa
Fri, 2018-06-29 07:54
Normal topic Fusing C-terminal or N-terminal segments onto proteins using Remodel
by achambe » Tue, 2016-01-05 09:39
1
2,513 by achambe
Wed, 2016-01-13 10:46
Normal topic GALigandDock errors
by Delfosse57 » Mon, 2023-08-07 13:16
0
488 by Delfosse57
Mon, 2023-08-07 13:16
Normal topic Gaussian Constraint For Dihedrals
by jinli711 » Thu, 2020-07-23 10:47
1
1,417 by matteoferla
Fri, 2020-07-24 03:06
Normal topic General Forum Suggestion
by jadolfbr » Thu, 2011-09-29 08:11
0
2,807 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic General Protein Folding Question
by twopint23oz » Sun, 2012-04-01 22:57
7
6,570 by smlewis
Mon, 2014-04-21 06:47
Normal topic General protein-protein docking when no info. on structure is availble
by jasnyderjr » Fri, 2016-12-09 04:55
3
3,278 by smlewis
Tue, 2016-12-20 10:40
Normal topic general question about protein docking
by albumns » Mon, 2010-12-13 23:26
1
2,503 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32
2
1,069 by Ken
Wed, 2022-08-17 08:04
Normal topic GeneralizedKIC side chain closure.
by almeida85 » Mon, 2022-09-19 06:13
0
615 by almeida85
Mon, 2022-09-19 07:22
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11
2
3,219 by Trentage
Mon, 2014-04-21 06:47
Normal topic Generate full symmetric assembly from subsystem
by lj269 » Thu, 2011-04-28 20:04
1
2,441 by IAndre
Mon, 2014-04-21 06:47
Normal topic Generate structural fragments
by kingljy » Tue, 2011-05-10 20:18
2
5,176 by pepfolder
Mon, 2014-04-21 06:47
Normal topic Generate template parameter file for a polymer
by anarob » Fri, 2022-06-10 11:05
1
772 by matteoferla
Fri, 2022-06-17 10:38
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44
2
2,624 by ndousis
Mon, 2014-04-21 06:47
Normal topic Generating Fragment Libraries for Metal Binding Proteins
by buzb » Wed, 2011-01-26 12:43
1
2,880 by kaue
Mon, 2014-04-21 06:47
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 Generating Protein/NA decoys
by rbeier1 » Mon, 2016-01-11 03:25
1
2,551 by rmoretti
Thu, 2016-04-28 16:25
Normal topic genkic mover produced an unwanted HN - CA bond
by cttm4a1 » Mon, 2022-06-20 14:25
2
1,016 by cttm4a1
Mon, 2022-06-20 16:58
Normal topic Get fasta from PDB script correction - Solved
by ialvy » Tue, 2022-08-30 00:00
0
560 by ialvy
Tue, 2022-08-30 00:00
Normal topic Get nchi for heavy atoms
by pachecoj » Tue, 2014-11-04 19:04
1
2,168 by rmoretti
Tue, 2014-11-11 13:22
Normal topic Getting an interface score from RosettaDock without docking
by rosend » Fri, 2015-12-18 14:02
3
6,538 by rosend
Fri, 2015-12-18 19:39
Normal topic Getting started with Rosetta
by myang » Tue, 2009-04-07 16:25
1
2,631 by smlewis
Mon, 2014-04-21 06:47
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31
3
3,601 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Give diferent chain information for a single sequence (comparative modeling)
by Martin Floor » Tue, 2013-04-02 08:59
4
4,792 by Martin Floor
Mon, 2014-04-21 06:47
Normal topic Give preference to native residue during fixed backbone designing
by tusharranjanmoharana » Mon, 2016-04-04 12:43
6
5,825 by rmoretti
Thu, 2016-04-28 15:19
Normal topic Global Docking with output analysis RMS
by kwu030 » Fri, 2024-02-23 09:17
1
269 by rmoretti
Mon, 2024-02-26 08:24
Normal topic Global ligand docking with Rosetta script and PyRosetta
by tisozaki » Tue, 2021-12-14 17:16
0
774 by tisozaki
Tue, 2021-12-14 17:16
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25
2
4,318 by rmoretti
Wed, 2015-01-21 10:05
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
628 by rmoretti
Mon, 2023-02-06 14:35
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
2,311 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Hamiltonian Exchange
by JSK » Mon, 2024-03-18 12:44
0
172 by JSK
Tue, 2024-03-19 09:21
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
3,578 by rmoretti
Mon, 2014-04-21 06:48
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57
2
2,618 by smlewis
Mon, 2014-04-21 06:47
Normal topic have trouble with "relax" models
by wszjzhang » Thu, 2010-01-28 10:02
1
2,167 by smlewis
Mon, 2014-04-21 06:47
Normal topic Having trouble producing a .pdb file from a silent output file after running abinitio relax
by burkheadlab » Wed, 2011-03-09 12:48
2
3,097 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
1,690 by rmoretti
Mon, 2018-03-19 09:08
Normal topic HBNetStapleInterface
by sdh_h » Wed, 2016-08-24 03:30
1
1,780 by smlewis
Wed, 2016-08-24 07:23
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17
3
3,855 by alejandro
Mon, 2014-04-21 06:47
Normal topic header pathways not accessable: No such file or directory
by rlwoltz » Tue, 2012-09-18 17:44
1
2,385 by smlewis
Mon, 2014-04-21 06:47
Normal topic Helical symmetry for cryo-EM refinement
by fmerino » Mon, 2017-10-16 04:02
0
1,426 by fmerino
Mon, 2017-10-16 04:02
Normal topic Helix at loop site
by berk » Fri, 2013-05-31 07:04
1
2,303 by smlewis
Mon, 2014-04-21 06:48
Normal topic Help - Protein-Protein interface design
by Dinesh Kumar » Thu, 2021-01-28 00:47
1
1,126 by rmoretti
Tue, 2021-02-09 10:29
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
2
1,376 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic Help with file in article Kemp elimination catalysts by computational enzyme design
by Wenithor » Sat, 2021-10-09 07:23
0
695 by Wenithor
Sat, 2021-10-09 07:23
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12
1
1,415 by rmoretti
Tue, 2021-02-09 12:35
Normal topic Help with get_pdb.py for PDB file cleaning
by lzx32 » Mon, 2011-03-28 02:11
7
9,121 by smlewis
Mon, 2014-04-21 06:47
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
3,184 by einew
Mon, 2014-04-21 06:47
Hot topic high resolution protein docking doesn't work
by albumns » Thu, 2010-12-02 02:36
17
14,312 by albumns
Mon, 2014-04-21 06:47
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51
2
3,112 by felipet
Sat, 2016-07-09 09:50
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
18,787 by rmoretti
Mon, 2018-01-15 15:37
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59
2
3,700 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Homology Model gives output - but completely wrong!
by Julix » Wed, 2012-10-31 10:10
1
3,364 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,748 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27
0
1,548 by gobli033
Mon, 2014-04-21 06:47
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56
3
3,453 by smlewis
Fri, 2016-07-29 07:43
Normal topic How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion
by wwwmrzkwww » Sun, 2021-08-15 00:19
0
830 by wwwmrzkwww
Sun, 2021-08-15 00:19
Normal topic How can move peptide on cleft of enzyme on Flexpepdock?
by phanvy » Thu, 2014-06-05 02:22
4
4,634 by zaldini
Fri, 2015-01-02 05:38
Normal topic How did you begin to learn Rosetta?
by mdeklotz » Mon, 2018-07-30 10:08
1
2,240 by jkleman
Tue, 2018-07-31 13:19
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30
6
13,863 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How do I add virtual atom to my cofactor (metal ion) in rosettadock?
by monos_morpheus » Sat, 2011-02-05 21:24
2
3,408 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic How do I implement more CPU cores in the execution of FlexPepDock?
by ChoripanSalado » Thu, 2024-05-02 08:55
0
133 by ChoripanSalado
Thu, 2024-05-02 08:55
Normal topic How do the homology sequences exclude from fragment files?
by exchhattu » Mon, 2010-04-05 03:04
1
2,107 by smlewis
Mon, 2014-04-21 06:47
Normal topic How do you implement phosphoserine in ab -initio folding?
by smiruthi » Fri, 2011-12-16 14:45
10
10,147 by brspurri
Mon, 2014-04-21 06:47
Normal topic How does one prevent Rosetta from connecting two separate chains?
by jhbrown » Thu, 2011-12-15 14:08
7
7,038 by Anonymous
Mon, 2014-04-21 06:47
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
1,502 by patcD
Wed, 2021-09-01 06:54
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
401 by JasonIsaac
Tue, 2023-05-02 03:39
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44
1
2,159 by rmoretti
Wed, 2015-02-18 09:19
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
929 by haom
Tue, 2020-09-01 18:50
Normal topic how same random seeds can be used in rosetta for mpi run.
by exchhattu » Wed, 2009-10-28 22:09
1
2,825 by smlewis
Mon, 2014-04-21 06:47
Normal topic How the Rosetta score (dG) is actually related to dH (enthalpy) and dS (entropy)?
by lanselibai » Thu, 2014-12-04 13:16
4
6,426 by lanselibai
Fri, 2014-12-12 10:27
Normal topic How to set the cyana format of distance restraint in rosetta?
by zhisheng » Mon, 2011-04-25 02:21
1
3,129 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to add constrains in flexible peptide docking
by kingbo2008 » Fri, 2011-04-29 07:55
1
2,401 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to add new Movers to Rosetta
by mb0261 » Thu, 2022-06-30 10:48
0
533 by mb0261
Thu, 2022-06-30 10:48
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08
4
1,164 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
4,159 by Jeffrey_Chen
Tue, 2014-03-25 23:06
Normal topic How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches
by zaldini » Fri, 2015-01-02 05:53
4
4,663 by zaldini
Wed, 2015-01-07 20:35
Normal topic how to build homology based models?
by albumns » Thu, 2010-06-24 10:27
0
1,514 by albumns
Mon, 2014-04-21 06:47
Normal topic How to calculate the binding energy of peptide and a protein?
by tianbu » Thu, 2014-02-13 20:44
9
11,399 by tianbu
Mon, 2014-02-17 03:36
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
6,551 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to convert fragments to PDB format?
by JadAbbass » Wed, 2015-08-19 04:05
1
2,244 by rmoretti
Wed, 2015-09-02 12:48
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
0
864 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic How to create a rotamer set that includes all possible rotamers of all possible amino acids
by AyushGoyal » Thu, 2014-11-06 10:37
1
2,492 by smlewis
Fri, 2014-11-07 12:03
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