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Rosetta 3 - Applications

Topic / Topic startersort descending Replies Views Last post
Normal topic How to add a residue to one chain of an existing structure?
by sn » Mon, 2017-04-17 09:34
2
3,190 by sn
Thu, 2017-04-20 21:43
Normal topic How to add additional rounds of design and optimization in Rosetta scripts?
by Nicole Deng » Tue, 2020-11-03 19:05
2
1,496 by Nicole Deng
Thu, 2020-11-05 03:04
Normal topic How to add constrains to FlexPepDocking?
by MajorID » Thu, 2011-06-02 11:00
2
3,251 by MajorID
Mon, 2014-04-21 06:47
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
1
1,407 by smlewis
Mon, 2019-09-16 12:22
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
0
924 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?
by lanselibai » Sat, 2015-01-17 11:19
1
3,135 by lanselibai
Wed, 2015-01-21 02:40
Normal topic How to calculate dG?
by yperez » Mon, 2012-10-22 07:28
1
3,038 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to change the axes of "-spin" in docking_protocol
by Zehui Zhou » Mon, 2023-02-13 22:06
0
2,067 by Zehui Zhou
Mon, 2023-02-13 22:06
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06
6
4,043 by chandana
Tue, 2022-08-09 20:27
Normal topic How to concatenate the 3-mer and 9-mer files for RosettaCM?
by lanselibai » Fri, 2020-05-08 05:38
5
3,228 by danpf
Tue, 2020-05-12 10:58
Normal topic how to control alignment for energy_based_clustering
by xfradera » Tue, 2023-02-28 10:13
0
1,804 by xfradera
Tue, 2023-02-28 10:13
Normal topic How to correctly incorporate constraint information into ab initio structure prediction?
by johnnytam100 » Tue, 2019-02-19 03:13
2
2,221 by johnnytam100
Fri, 2019-03-01 01:36
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
2
1,707 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic How to define pi-pi stacking in cst file?
by lzx32 » Mon, 2011-07-04 23:47
6
8,078 by lzx32
Mon, 2014-04-21 06:47
Normal topic How to design the anitgen-antibody interface
by Sunyp_IM » Tue, 2017-12-12 18:44
0
1,206 by Sunyp_IM
Tue, 2017-12-12 18:44
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
5
5,038 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
2,976 by lanselibai
Fri, 2014-10-17 03:36
Normal topic How to estimate the effect of a mutation on the binding energy?
by ltrabuco » Tue, 2011-02-15 08:02
4
5,390 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to find cluster core structure?
by assignfit » Thu, 2012-03-29 20:35
7
7,256 by attesor
Wed, 2017-06-14 07:32
Normal topic how to find help informations on rosetta_scripts in rosetta3.10
by xinmiaohe » Mon, 2019-08-26 14:48
5
3,099 by xinmiaohe
Tue, 2019-08-27 08:37
Normal topic how to fix the ATP HETATM by using movemap or constraint file?
by ziqi1234 » Mon, 2017-11-20 06:43
9
6,855 by ziqi1234
Wed, 2017-11-22 06:21
Normal topic How to freeze ligand during FastRelax?
by dnamkr » Thu, 2020-01-02 14:53
1
1,556 by aloshbau
Fri, 2020-01-10 16:48
Normal topic how to generate the whole molecule that contains all the symmetric chains
by Sunyp_IM » Sun, 2017-12-10 19:43
0
1,202 by Sunyp_IM
Sun, 2017-12-10 19:43
Normal topic how to know the precedure of solving a actural bio problem? like interface design?
by qq7678500549 » Thu, 2020-08-06 18:45
2
1,530 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic how to make "static" built binaries use multiple cpus like "mpi"?
by Danielsebas » Wed, 2019-09-18 06:41
3
2,579 by rmoretti
Wed, 2019-09-18 10:21
Normal topic How to make new VALL database?
by Danielsebas » Sun, 2019-09-08 02:16
2
2,480 by Danielsebas
Wed, 2019-09-11 00:44
Normal topic How to minimize the decoys obtained from backrub?
by Vedasheersh » Wed, 2017-06-14 10:26
5
4,205 by SenyorDrew
Fri, 2017-06-30 09:47
Normal topic How to model missing residues on a protein from multiple PDB files?
by cossio » Fri, 2015-08-21 07:18
6
13,109 by rmoretti
Fri, 2015-09-11 13:27
Normal topic How to only constructure the tail conformation when using "FloppyTail.linuxgccrelease"?
by lanselibai » Mon, 2014-10-13 10:26
5
5,522 by lanselibai
Wed, 2014-10-15 03:52
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40
4
4,843 by cossio
Mon, 2015-01-19 07:10
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37
3
3,726 by rmoretti
Tue, 2017-10-10 09:58
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05
2
1,963 by dnamkr
Fri, 2022-04-22 17:00
Normal topic how to pick fragments for a transmembrane protein
by tevang » Mon, 2012-05-28 06:52
1
2,248 by tevang
Mon, 2014-04-21 06:47
Normal topic How to preserve ACE/NME termini?
by nitroamos » Tue, 2018-05-22 13:07
3
3,693 by rmoretti
Thu, 2018-06-28 12:44
Normal topic how to reconstruct the whole complex after symmetric docking
by Anonymous » Tue, 2012-07-03 02:44
2
3,242 by felipet
Wed, 2014-07-02 07:26
Normal topic how to repacking loop while freezing other residues?
by jfhuang » Wed, 2012-07-25 06:59
10
8,724 by jfhuang
Mon, 2014-04-21 06:47
Normal topic How to restart RASREC run
by aep » Fri, 2016-07-01 04:39
2
2,414 by aep
Fri, 2016-07-01 06:54
Normal topic how to run ala_scan.xml
by xinmiaohe » Mon, 2019-08-26 09:38
0
1,064 by xinmiaohe
Mon, 2019-08-26 09:38
Normal topic how to run my openmp programe in rosetta3.3?
by lihowe » Mon, 2012-02-27 23:43
1
2,400 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to run partial_thread in RosettaCM when residure are more than 9999?
by lanselibai » Mon, 2020-05-11 22:43
2
2,144 by lanselibai
Tue, 2020-05-12 20:25
Normal topic How to scan double mutations in RosettaScripts?
by msardejani » Mon, 2016-12-12 16:52
2
2,471 by msardejani
Mon, 2016-12-12 17:48
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
1
1,176 by ssrb
Mon, 2020-06-22 13:12
Normal topic How to sort a Silent File based on RMSD
by JadAbbass » Sun, 2013-08-04 14:40
2
3,540 by lanselibai
Mon, 2014-10-06 15:30
Normal topic How to specify only design surface residues and loops by RosettaScripts?
by johnnytam100 » Sun, 2019-04-07 21:47
4
3,060 by johnnytam100
Wed, 2019-04-10 02:48
Normal topic How to use -cst_fa_file and -relax:constrain_relax_to_native_coords at the same time
by Anatol » Thu, 2012-11-29 14:12
11
10,472 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
1,079 by everyday847
Sun, 2021-04-04 12:48
Normal topic How to use MHC Epitope energy (mhc_epitope) to deimmunize a protein structure?
by Sunyp_IM » Sun, 2020-11-08 08:07
5
3,064 by Brahm Yachnin
Wed, 2020-11-18 17:21
Normal topic How to use Rosetta to DISCARD a protein-protein docking interface?
by cossio » Tue, 2015-05-26 06:24
2
3,193 by rmoretti
Sat, 2015-07-11 13:38
Normal topic How to write down a connection between ligand's atom and metal ion from enzyme?
by Corvin » Mon, 2021-02-15 06:54
7
3,429 by aloshbau
Mon, 2021-03-01 20:06
Normal topic How tu use Delta filter's relax_mover
by pocin » Sun, 2017-02-19 05:21
3
3,257 by rmoretti
Wed, 2017-03-01 13:10
Normal topic hpatch commands and how to identify patches
by Bianca Oliva » Thu, 2021-04-29 04:02
0
915 by Bianca Oliva
Thu, 2021-04-29 04:02
Normal topic hybrid approach - comparative and ab initio modelling
by eprates » Wed, 2019-03-20 11:58
1
1,468 by rmoretti
Fri, 2019-03-29 09:45
Normal topic I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes
by Wenithor » Thu, 2022-01-06 12:20
0
1,011 by Wenithor
Thu, 2022-01-06 12:20
Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
1,243 by leygkn
Tue, 2020-09-22 22:46
Normal topic I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi
by Edward » Sat, 2023-11-25 04:58
1
277 by Edward
Sat, 2023-11-25 05:17
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
3,196 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic If "clustering.py" can be used for PDBs contain two chains?
by lanselibai » Wed, 2014-11-05 06:05
7
7,097 by lanselibai
Tue, 2014-12-02 09:43
Normal topic IL-2 gets better binding with beta / gamma
by tonycheng1688 » Wed, 2022-05-25 10:23
0
881 by tonycheng1688
Wed, 2022-05-25 10:23
Normal topic Imitating induced fit protocol in SymDock2 without any symmetry constraints
by chenna » Fri, 2020-02-14 01:35
2
1,914 by chenna
Wed, 2020-03-04 03:24
Normal topic in silico affinity maturation design
by jarod » Mon, 2013-05-20 02:07
11
12,385 by jarod
Mon, 2014-04-21 06:47
Normal topic Include MHC alpha helices in loop modelling protocol for pMHC complex
by Roberto » Thu, 2022-08-04 07:22
0
812 by Roberto
Thu, 2022-08-04 07:22
Normal topic Including ab-initio predicted model in fragment library generation
by ashu4487 » Thu, 2016-12-08 17:49
2
2,395 by ashu4487
Sun, 2016-12-11 19:03
Normal topic Including waters in RosettaCM
by ajkal » Thu, 2017-04-27 11:59
9
7,619 by rpavlov
Tue, 2017-06-06 11:45
Normal topic Incorporating iron-sulfur cluster into ROSETTA applications
by Derek Smith » Thu, 2014-08-14 23:12
1
2,669 by rmoretti
Fri, 2014-08-15 08:06
Normal topic Incorrect Jump being set in RosettaScripts docking mover
by weehee » Fri, 2012-06-08 10:23
6
7,579 by rmoretti
Mon, 2014-04-21 06:47
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
1,457 by rmoretti
Tue, 2019-04-16 11:07
Normal topic Input structure
by Soler » Mon, 2020-09-28 13:18
1
1,097 by ssrb
Tue, 2020-09-29 12:37
Normal topic Inquiry about MPI-Rosetta: Issue with -nstruct Parameter
by serena » Wed, 2024-01-24 00:59
1
123 by rmoretti
Wed, 2024-01-24 08:46
Normal topic Inserting residues using RosettaRemodel
by eleishaj » Tue, 2015-11-24 08:54
7
8,374 by eyong123
Wed, 2015-12-09 07:17
Normal topic Instructing design scripts to use noncanonical AA instead of canonical
by zcrook » Tue, 2014-11-25 10:43
1
2,110 by rmoretti
Wed, 2014-11-26 07:51
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
0
1,131 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
2,278 by smlewis
Tue, 2017-02-21 14:10
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,885 by smlewis
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer dSasa calculation
by mintseris » Wed, 2015-09-02 09:43
2
4,427 by jadolfbr
Thu, 2015-09-03 16:18
Normal topic InterfaceAnalyzer problem
by almeida » Mon, 2014-03-03 14:56
3
4,916 by smlewis
Fri, 2014-03-07 14:09
Normal topic InterfaceAnalyzer:“too many tries in fill_missing_atoms!”
by mxp » Tue, 2019-08-06 00:41
8
6,621 by mxp
Mon, 2019-08-12 18:42
Normal topic interface_delta ligand_docking
by Prasanth Kumar » Tue, 2013-06-18 08:37
1
2,654 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Is Biopython required to run pdb_renumber.py?
by ljjjxay » Wed, 2023-11-22 20:00
6
561 by ljjjxay
Wed, 2023-12-06 19:24
Normal topic is it necessary to always run relax before any Rosetta
by mainzer » Fri, 2019-04-12 01:35
1
1,955 by rmoretti
Wed, 2019-07-10 09:47
Normal topic Is it possible to restart the ddg_monomer.linuxgccrelease?
by lanselibai » Mon, 2015-09-07 03:46
1
2,102 by rmoretti
Wed, 2015-09-09 12:01
Normal topic Is native.pdb necess for fragment_picker?
by ylwang » Thu, 2020-03-12 00:57
2
1,850 by ylwang
Thu, 2020-03-12 20:42
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35
5
5,163 by rmoretti
Mon, 2015-02-09 12:04
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
1,371 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic issues about cstfile in RosettaMatch
by Nicole Deng » Fri, 2020-12-18 05:44
3
2,677 by He Xiao
Sun, 2021-04-11 19:29
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
0
751 by DGR95
Fri, 2021-05-14 12:51
Normal topic JD2 MPI
by jrcf » Wed, 2015-10-28 14:45
1
2,338 by rmoretti
Sat, 2015-10-31 08:57
Normal topic jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease
by fradom » Mon, 2017-11-27 02:55
6
4,858 by fradom
Tue, 2017-12-05 01:52
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
3,373 by Wizard
Sun, 2015-04-26 22:36
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
1,494 by bjharris
Wed, 2020-07-01 23:25
Normal topic KeyError: 'subject-id' in antibody modelling
by bogac » Mon, 2017-03-06 02:00
2
3,087 by bogac
Tue, 2017-03-07 02:11
Normal topic KIC with fragments versus Next generation KIC
by Loki01 » Fri, 2018-09-07 05:06
3
2,892 by smlewis
Mon, 2018-09-10 11:48
Normal topic kinematic loop modeling multiple input: possible?
by a_s_a » Thu, 2011-05-12 09:33
2
3,317 by a_s_a
Mon, 2014-04-21 06:47
Normal topic Lammps or RosettaSurface
by StevPChem » Fri, 2016-06-10 10:13
3
3,893 by Anpu
Tue, 2018-09-25 18:53
Normal topic latest version of rosetta unable to build models
by pramod » Mon, 2014-11-03 11:31
1
2,830 by rmoretti
Tue, 2014-11-04 10:33
Normal topic Ligand atom RMSD calculation
by lkrathn » Wed, 2013-08-14 21:25
2
4,649 by lkrathn
Mon, 2014-04-21 06:48
Normal topic ligand conformer generation for enzyme design
by bo » Mon, 2013-02-11 16:51
1
2,435 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ligand creation
by Prasanth Kumar » Fri, 2013-08-02 09:48
1
2,434 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Ligand dock analysis
by sacch » Tue, 2012-05-22 01:20
3
3,861 by glemmon
Mon, 2014-04-21 06:47
Normal topic ligand dock into HEM containg pdb
by syntekabio2019 » Thu, 2022-01-20 03:05
0
1,005 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49
4
4,451 by sacch
Mon, 2014-04-21 06:47
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