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Rosetta 3 - Applications

Topic / Topic startersort ascending Replies Views Last post
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
0
1,000 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
0
939 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic ligand_docking tutorial help: do crystal_complex.pdb files need to be prepped before using with <InterfaceScoreCalculator>
by DGR95 » Fri, 2021-04-16 19:26
4
2,453 by DGR95
Wed, 2021-04-28 16:13
Normal topic ligand_docking ligand preparation
by Alison_Yajie » Thu, 2020-05-21 10:21
2
1,713 by Alison_Yajie
Wed, 2020-06-24 12:38
Normal topic ligand_docking
by yang » Thu, 2023-02-16 04:37
2
2,595 by yang
Wed, 2023-02-22 19:18
Normal topic Ligand Rotamer Control in Macther
by Hirbond » Tue, 2022-10-25 13:01
0
1,808 by Hirbond
Wed, 2022-10-26 12:57
Normal topic Ligand params file proton_chi parameters
by staciekim » Thu, 2017-08-17 14:50
2
3,191 by staciekim
Thu, 2017-08-17 17:06
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
2,698 by rmoretti
Mon, 2014-05-12 15:08
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
3,071 by jharamesh
Mon, 2014-11-03 12:50
Normal topic ligand docking, how to combine some silent.out files into a silent_all.out file
by Ryhon Wang » Fri, 2013-12-06 01:53
6
7,519 by rmoretti
Wed, 2017-01-11 12:53
Normal topic Ligand Docking with RosettaScripts gives a ParsedProtocol exception
by brspurri » Sun, 2017-05-14 17:51
2
3,112 by brspurri
Mon, 2017-05-15 11:48
Normal topic Ligand Docking with Rosetta Scripts memory problem
by Swillard » Thu, 2017-08-17 14:59
5
5,054 by rmoretti
Mon, 2018-11-12 14:31
Normal topic Ligand Docking with ROSETTA
by sc19 » Thu, 2022-07-14 01:32
0
1,018 by sc19
Thu, 2022-07-14 01:34
Normal topic ligand docking with MPI
by Ruska322 » Wed, 2019-09-04 03:47
2
1,864 by Ruska322
Fri, 2019-09-06 07:13
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
0
901 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic Ligand Docking with ARLS
by cam11 » Thu, 2016-06-23 09:34
1
2,233 by rmoretti
Thu, 2016-06-23 10:55
Normal topic Ligand docking cannot open the protein file
by swarekwood » Tue, 2017-10-17 08:17
1
1,673 by rmoretti
Tue, 2017-10-17 09:03
Normal topic Ligand docking at specific orientation
by ShiranBZ » Mon, 2020-04-13 20:46
1
1,286 by matteoferla
Mon, 2020-05-04 02:02
Normal topic Ligand docking and protein design of an internal pocket in a protein with a cofactor
by oerbilgin » Mon, 2011-06-20 13:55
2
4,930 by frichter
Mon, 2014-04-21 06:47
Normal topic ligand dock question
by sacch » Sun, 2012-05-20 19:49
4
4,650 by sacch
Mon, 2014-04-21 06:47
Normal topic ligand dock into HEM containg pdb
by syntekabio2019 » Thu, 2022-01-20 03:05
0
1,077 by syntekabio2019
Thu, 2022-01-20 03:05
Normal topic Ligand dock analysis
by sacch » Tue, 2012-05-22 01:20
3
3,982 by glemmon
Mon, 2014-04-21 06:47
Normal topic Ligand creation
by Prasanth Kumar » Fri, 2013-08-02 09:48
1
2,503 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ligand conformer generation for enzyme design
by bo » Mon, 2013-02-11 16:51
1
2,531 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ligand atom RMSD calculation
by lkrathn » Wed, 2013-08-14 21:25
2
4,780 by lkrathn
Mon, 2014-04-21 06:48
Normal topic latest version of rosetta unable to build models
by pramod » Mon, 2014-11-03 11:31
1
2,949 by rmoretti
Tue, 2014-11-04 10:33
Normal topic Lammps or RosettaSurface
by StevPChem » Fri, 2016-06-10 10:13
3
4,066 by Anpu
Tue, 2018-09-25 18:53
Normal topic kinematic loop modeling multiple input: possible?
by a_s_a » Thu, 2011-05-12 09:33
2
3,423 by a_s_a
Mon, 2014-04-21 06:47
Normal topic KIC with fragments versus Next generation KIC
by Loki01 » Fri, 2018-09-07 05:06
3
3,036 by smlewis
Mon, 2018-09-10 11:48
Normal topic KeyError: 'subject-id' in antibody modelling
by bogac » Mon, 2017-03-06 02:00
2
3,207 by bogac
Tue, 2017-03-07 02:11
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
1
1,582 by bjharris
Wed, 2020-07-01 23:25
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
3,515 by Wizard
Sun, 2015-04-26 22:36
Normal topic jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease
by fradom » Mon, 2017-11-27 02:55
6
5,096 by fradom
Tue, 2017-12-05 01:52
Normal topic JD2 MPI
by jrcf » Wed, 2015-10-28 14:45
1
2,423 by rmoretti
Sat, 2015-10-31 08:57
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
0
820 by DGR95
Fri, 2021-05-14 12:51
Normal topic issues about cstfile in RosettaMatch
by Nicole Deng » Fri, 2020-12-18 05:44
3
2,894 by He Xiao
Sun, 2021-04-11 19:29
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
1,449 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35
5
5,364 by rmoretti
Mon, 2015-02-09 12:04
Normal topic Is native.pdb necess for fragment_picker?
by ylwang » Thu, 2020-03-12 00:57
2
1,984 by ylwang
Thu, 2020-03-12 20:42
Normal topic Is it possible to restart the ddg_monomer.linuxgccrelease?
by lanselibai » Mon, 2015-09-07 03:46
1
2,193 by rmoretti
Wed, 2015-09-09 12:01
Normal topic is it necessary to always run relax before any Rosetta
by mainzer » Fri, 2019-04-12 01:35
1
2,093 by rmoretti
Wed, 2019-07-10 09:47
Normal topic Is Biopython required to run pdb_renumber.py?
by ljjjxay » Wed, 2023-11-22 20:00
6
952 by ljjjxay
Wed, 2023-12-06 19:24
Normal topic interface_delta ligand_docking
by Prasanth Kumar » Tue, 2013-06-18 08:37
1
2,734 by rmoretti
Mon, 2014-04-21 06:48
Normal topic InterfaceAnalyzer:“too many tries in fill_missing_atoms!”
by mxp » Tue, 2019-08-06 00:41
8
7,168 by mxp
Mon, 2019-08-12 18:42
Normal topic InterfaceAnalyzer problem
by almeida » Mon, 2014-03-03 14:56
3
5,071 by smlewis
Fri, 2014-03-07 14:09
Normal topic InterfaceAnalyzer dSasa calculation
by mintseris » Wed, 2015-09-02 09:43
2
4,601 by jadolfbr
Thu, 2015-09-03 16:18
Normal topic InterfaceAnalyzer -resfile
by gw » Wed, 2011-11-02 16:01
1
2,986 by smlewis
Mon, 2014-04-21 06:47
Normal topic Interface Analyzer Segmentation Fault
by h_trasatti » Tue, 2017-02-21 12:48
1
2,368 by smlewis
Tue, 2017-02-21 14:10
Normal topic Interesting scoring performance in flexpepdock against random peptides
by ziqi1234 » Fri, 2017-12-08 07:52
0
1,192 by ziqi1234
Fri, 2017-12-08 07:52
Normal topic Instructing design scripts to use noncanonical AA instead of canonical
by zcrook » Tue, 2014-11-25 10:43
1
2,203 by rmoretti
Wed, 2014-11-26 07:51
Normal topic Inserting residues using RosettaRemodel
by eleishaj » Tue, 2015-11-24 08:54
7
8,736 by eyong123
Wed, 2015-12-09 07:17
Normal topic Inquiry about MPI-Rosetta: Issue with -nstruct Parameter
by serena » Wed, 2024-01-24 00:59
1
327 by rmoretti
Wed, 2024-01-24 08:46
Normal topic Input structure
by Soler » Mon, 2020-09-28 13:18
1
1,181 by ssrb
Tue, 2020-09-29 12:37
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
1,552 by rmoretti
Tue, 2019-04-16 11:07
Normal topic Incorrect Jump being set in RosettaScripts docking mover
by weehee » Fri, 2012-06-08 10:23
6
7,827 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Incorporating iron-sulfur cluster into ROSETTA applications
by Derek Smith » Thu, 2014-08-14 23:12
1
2,787 by rmoretti
Fri, 2014-08-15 08:06
Normal topic Including waters in RosettaCM
by ajkal » Thu, 2017-04-27 11:59
9
7,974 by rpavlov
Tue, 2017-06-06 11:45
Normal topic Including ab-initio predicted model in fragment library generation
by ashu4487 » Thu, 2016-12-08 17:49
2
2,502 by ashu4487
Sun, 2016-12-11 19:03
Normal topic Include MHC alpha helices in loop modelling protocol for pMHC complex
by Roberto » Thu, 2022-08-04 07:22
0
880 by Roberto
Thu, 2022-08-04 07:22
Normal topic in silico affinity maturation design
by jarod » Mon, 2013-05-20 02:07
11
12,785 by jarod
Mon, 2014-04-21 06:47
Normal topic Imitating induced fit protocol in SymDock2 without any symmetry constraints
by chenna » Fri, 2020-02-14 01:35
2
2,040 by chenna
Wed, 2020-03-04 03:24
Normal topic IL-2 gets better binding with beta / gamma
by tonycheng1688 » Wed, 2022-05-25 10:23
0
945 by tonycheng1688
Wed, 2022-05-25 10:23
Normal topic If "clustering.py" can be used for PDBs contain two chains?
by lanselibai » Wed, 2014-11-05 06:05
7
7,364 by lanselibai
Tue, 2014-12-02 09:43
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
3,310 by jadolfbr
Mon, 2014-04-21 06:47
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
450 by Edward
Sat, 2023-11-25 05:17
Normal topic I need some help for using pHDock applications(histidine protonation / pH-dependent binding)
by leygkn » Tue, 2020-09-22 18:40
1
1,365 by leygkn
Tue, 2020-09-22 22:46
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
1,153 by Wenithor
Thu, 2022-01-06 12:20
Normal topic hybrid approach - comparative and ab initio modelling
by eprates » Wed, 2019-03-20 11:58
1
1,563 by rmoretti
Fri, 2019-03-29 09:45
Normal topic hpatch commands and how to identify patches
by Bianca Oliva » Thu, 2021-04-29 04:02
0
1,011 by Bianca Oliva
Thu, 2021-04-29 04:02
Normal topic How tu use Delta filter's relax_mover
by pocin » Sun, 2017-02-19 05:21
3
3,417 by rmoretti
Wed, 2017-03-01 13:10
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
3,768 by aloshbau
Mon, 2021-03-01 20:06
Normal topic How to use Rosetta to DISCARD a protein-protein docking interface?
by cossio » Tue, 2015-05-26 06:24
2
3,333 by rmoretti
Sat, 2015-07-11 13:38
Normal topic How to use rewrite_rosetta_script.py to update XML script file?
by intomybioverse » Fri, 2024-03-15 06:44
2
285 by intomybioverse
Sun, 2024-03-17 06:22
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
3,299 by Brahm Yachnin
Wed, 2020-11-18 17:21
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
1,175 by everyday847
Sun, 2021-04-04 12:48
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
10,898 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to specify only design surface residues and loops by RosettaScripts?
by johnnytam100 » Sun, 2019-04-07 21:47
4
3,293 by johnnytam100
Wed, 2019-04-10 02:48
Normal topic How to sort a Silent File based on RMSD
by JadAbbass » Sun, 2013-08-04 14:40
2
3,665 by lanselibai
Mon, 2014-10-06 15:30
Normal topic How to select docked models
by Sunyp_IM » Mon, 2020-06-22 00:50
1
1,261 by ssrb
Mon, 2020-06-22 13:12
Normal topic How to scan double mutations in RosettaScripts?
by msardejani » Mon, 2016-12-12 16:52
2
2,579 by msardejani
Mon, 2016-12-12 17:48
Normal topic How to run partial_thread in RosettaCM when residure are more than 9999?
by lanselibai » Mon, 2020-05-11 22:43
2
2,315 by lanselibai
Tue, 2020-05-12 20:25
Normal topic how to run my openmp programe in rosetta3.3?
by lihowe » Mon, 2012-02-27 23:43
1
2,468 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to run ala_scan.xml
by xinmiaohe » Mon, 2019-08-26 09:38
0
1,156 by xinmiaohe
Mon, 2019-08-26 09:38
Normal topic How to restart RASREC run
by aep » Fri, 2016-07-01 04:39
2
2,536 by aep
Fri, 2016-07-01 06:54
Normal topic how to repacking loop while freezing other residues?
by jfhuang » Wed, 2012-07-25 06:59
10
9,053 by jfhuang
Mon, 2014-04-21 06:47
Normal topic how to reconstruct the whole complex after symmetric docking
by Anonymous » Tue, 2012-07-03 02:44
2
3,351 by felipet
Wed, 2014-07-02 07:26
Normal topic How to preserve ACE/NME termini?
by nitroamos » Tue, 2018-05-22 13:07
3
3,875 by rmoretti
Thu, 2018-06-28 12:44
Normal topic how to pick fragments for a transmembrane protein
by tevang » Mon, 2012-05-28 06:52
1
2,335 by tevang
Mon, 2014-04-21 06:47
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05
2
2,177 by dnamkr
Fri, 2022-04-22 17:00
Normal topic How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI
by kingljy » Sun, 2017-09-24 18:37
3
3,916 by rmoretti
Tue, 2017-10-10 09:58
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40
4
5,034 by cossio
Mon, 2015-01-19 07:10
Normal topic How to only constructure the tail conformation when using "FloppyTail.linuxgccrelease"?
by lanselibai » Mon, 2014-10-13 10:26
5
5,748 by lanselibai
Wed, 2014-10-15 03:52
Normal topic How to model missing residues on a protein from multiple PDB files?
by cossio » Fri, 2015-08-21 07:18
6
13,548 by rmoretti
Fri, 2015-09-11 13:27
Normal topic How to minimize the decoys obtained from backrub?
by Vedasheersh » Wed, 2017-06-14 10:26
5
4,417 by SenyorDrew
Fri, 2017-06-30 09:47
Normal topic How to make new VALL database?
by Danielsebas » Sun, 2019-09-08 02:16
2
2,623 by Danielsebas
Wed, 2019-09-11 00:44
Normal topic how to make "static" built binaries use multiple cpus like "mpi"?
by Danielsebas » Wed, 2019-09-18 06:41
3
2,743 by rmoretti
Wed, 2019-09-18 10:21
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
1,639 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic how to generate the whole molecule that contains all the symmetric chains
by Sunyp_IM » Sun, 2017-12-10 19:43
0
1,259 by Sunyp_IM
Sun, 2017-12-10 19:43
Normal topic How to freeze ligand during FastRelax?
by dnamkr » Thu, 2020-01-02 14:53
1
1,676 by aloshbau
Fri, 2020-01-10 16:48
Normal topic how to fix the ATP HETATM by using movemap or constraint file?
by ziqi1234 » Mon, 2017-11-20 06:43
9
7,300 by ziqi1234
Wed, 2017-11-22 06:21
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