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Rosetta 3 - Applications

Topic / Topic starter Repliessort descending Views Last post
Normal topic terminal amino acids of gap has incomplete valency
by malkeet.singh » Wed, 2017-11-29 05:20 		6
 4,783 by rmoretti
Fri, 2017-12-01 12:05
Normal topic How to choose designed antibody
by Sunyp_IM » Wed, 2020-06-24 10:06 		6
 4,506 by chandana
Tue, 2022-08-09 20:27
Normal topic Docking with constraints
by ytao » Tue, 2013-04-02 09:45 		6
 8,230 by smlewis
Mon, 2014-04-21 06:47
Normal topic the ddg of mutant is same as the wt
by deepanshuiitb » Wed, 2015-03-04 11:56 		6
 6,978 by jadolfbr
Tue, 2015-04-07 10:50
Normal topic Problem with hotspot constraints.
by jarek » Wed, 2012-10-17 03:22 		6
 6,084 by xfliu
Mon, 2014-04-21 06:47
Normal topic symmetric design in the presence of a nonsymmetric ligand
by msardejani » Fri, 2016-09-30 15:17 		6
 6,476 by msardejani
Sat, 2016-10-01 12:55
Normal topic protein docking failed
by albumns » Thu, 2012-11-08 02:59 		6
 6,419 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Make error during installation of updated ncbi-blast-2.9.0+-src plus error with nr-database
by Corvin » Tue, 2019-10-01 02:04 		6
 6,564 by Corvin
Tue, 2019-10-15 01:12
Normal topic Loop modeling - the appropriate way to model a peptide insertion?
by xding » Thu, 2018-08-02 15:30 		6
 5,079 by smlewis
Wed, 2018-08-08 15:48
Normal topic the flexpepdock refinement and ab-initio
by tfliu » Mon, 2013-12-23 19:17 		6
 6,676 by tfliu
Mon, 2014-04-21 06:48
Normal topic Error src/core/scoring/MembraneTopology.cc line: 139
by Daniel Hall » Thu, 2017-07-13 04:58 		6
 6,239 by rmoretti
Tue, 2017-07-18 09:00
Normal topic Translate mover chain X doesnot exist.
by surya » Thu, 2020-07-09 08:36 		6
 3,607 by rmoretti
Tue, 2020-07-14 10:54
Normal topic docking in rosetta 3.3
by Ammu » Thu, 2012-03-15 12:03 		6
 6,331 by smlewis
Mon, 2014-04-21 06:47
Normal topic Abinitio doesn't run but does not give output or error
by Irving » Fri, 2016-10-28 10:04 		6
 6,105 by rmoretti
Mon, 2017-01-23 08:52
Normal topic jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease
by fradom » Mon, 2017-11-27 02:55 		6
 5,171 by fradom
Tue, 2017-12-05 01:52
Normal topic fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
by yueyuedake » Wed, 2023-07-12 03:36 		6
 1,414 by yueyuedake
Sun, 2023-07-16 19:17
Normal topic How to define pi-pi stacking in cst file?
by lzx32 » Mon, 2011-07-04 23:47 		6
 8,430 by lzx32
Mon, 2014-04-21 06:47
Normal topic Relax a structure with >1 copy of a modified residue fails [Solved]
by franfdez » Wed, 2012-02-08 00:47 		6
 6,705 by franfdez
Mon, 2014-04-21 06:47
Normal topic Running Rosetta CM Hybridize step errors with: Scorefunction not set up for nonideal/Cartesian scoring
by brspurri » Wed, 2017-03-29 13:19 		7
 6,780 by matteoferla
Mon, 2021-07-19 06:13
Normal topic protein structure prediction using relax -- high-powered jobs
by rfieldhouse » Mon, 2011-05-30 18:29 		7
 8,031 by dimaio
Mon, 2014-04-21 06:47
Normal topic Abinitio Relax Error from -kill_hairpins
by attesor » Tue, 2014-10-28 05:33 		7
 7,887 by rmoretti
Tue, 2014-11-04 10:28
Normal topic How to find cluster core structure?
by assignfit » Thu, 2012-03-29 20:35 		7
 7,688 by attesor
Wed, 2017-06-14 07:32
Normal topic neutral N-term and C-term
by nawsad » Sun, 2013-06-09 10:20 		7
 9,397 by helenah
Thu, 2020-10-08 05:29
Normal topic Inserting residues using RosettaRemodel
by eleishaj » Tue, 2015-11-24 08:54 		7
 8,828 by eyong123
Wed, 2015-12-09 07:17
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
 3,872 by aloshbau
Mon, 2021-03-01 20:06
Normal topic suppress pdb output from backrub
by attesor » Mon, 2014-10-27 11:16 		7
 7,494 by rmoretti
Mon, 2014-11-03 15:47
Normal topic If "clustering.py" can be used for PDBs contain two chains?
by lanselibai » Wed, 2014-11-05 06:05 		7
 7,453 by lanselibai
Tue, 2014-12-02 09:43
Normal topic Ensemble Docking in Rosetta3.5?
by protos_heis » Fri, 2015-05-22 06:42 		7
 8,895 by protos_heis
Mon, 2015-06-08 07:00
Normal topic where is pdb2vall.py
by tevang » Thu, 2013-01-24 13:35 		7
 7,346 by dktest
Mon, 2014-04-21 06:47
Normal topic "ddg_monomer.linuxgccrelease" by following "High Resolution Protocol"
by lanselibai » Wed, 2014-10-01 09:54 		7
 11,179 by lanselibai
Sat, 2015-01-03 08:18
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Sun, 2011-02-13 20:34 		7
 7,199 by yarovoy
Mon, 2014-04-21 06:47
Normal topic ddg_monomer consumes massive RAM
by cossio » Fri, 2018-03-09 17:02 		7
 6,659 by rmoretti
Mon, 2018-03-19 12:12
Normal topic modeling phosphorylated residue
by rosetter » Fri, 2011-03-18 08:13 		7
 8,888 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaRemodel can not work now?
by myputer » Tue, 2013-08-13 16:56 		7
 7,812 by rmoretti
Mon, 2014-04-21 06:48
Normal topic About scorefunction.
by Run » Mon, 2013-09-09 23:08 		7
 7,942 by rmoretti
Mon, 2014-04-21 06:48
Normal topic variable length fragments for Ab initio
by attesor » Wed, 2015-07-01 06:13 		7
 7,358 by rmoretti
Tue, 2015-08-18 16:47
Normal topic Problem about energy score
by tfliu » Tue, 2013-11-05 02:09 		7
 8,050 by Ora Schueler-Furman
Mon, 2014-04-21 06:48
Normal topic Rosetta scoring
by Dimitrov » Thu, 2012-09-20 01:54 		7
 10,276 by attesor
Mon, 2014-04-21 06:47
Normal topic How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?
by lanselibai » Tue, 2014-11-04 14:56 		7
 8,087 by lanselibai
Wed, 2014-11-12 11:17
Normal topic ERROR: Unable to fill in missing atoms.
by mieczyslaw » Tue, 2020-10-20 09:43 		7
 6,847 by rayyoung
Thu, 2021-11-18 10:13
Normal topic segmentation fault after core.kinematics.FoldTree in homology modeling
by pdbb » Mon, 2012-10-08 14:27 		7
 7,808 by rmoretti
Mon, 2014-04-21 06:47
Normal topic SnugDocking a VHH:antigen complex possible?
by David Weis » Thu, 2017-02-16 05:57 		7
 6,363 by rmoretti
Thu, 2017-07-06 13:00
Normal topic Can rosetta generate a centroid model based on the rna sequence?
by yels » Fri, 2021-03-26 04:06 		7
 3,405 by yels
Wed, 2021-03-31 18:31
Normal topic H3 modeling takes 10 days more?
by jessye » Fri, 2017-10-27 03:11 		7
 5,638 by jessye
Fri, 2017-11-03 20:15
Normal topic Write one's own constraint type
by djpittdj » Thu, 2012-11-08 12:29 		7
 6,948 by smlewis
Mon, 2014-04-21 06:47
Normal topic running in MPI mode and multiple scores per output PDB file?
by dantimatter » Wed, 2019-10-30 09:42 		7
 5,504 by dantimatter
Wed, 2019-11-06 09:51
Normal topic to create the template pdb file
by benniu2004 » Sat, 2012-12-29 23:04 		8
 8,977 by benniu2004
Mon, 2014-04-21 06:47
Normal topic Question about running scallo
by danbo » Mon, 2021-11-29 23:25 		8
 3,889 by danbo
Wed, 2021-12-22 23:51
Normal topic Multistate design on Rosetta - no generations produced
by tong » Wed, 2018-06-13 00:36 		8
 5,829 by smlewis
Thu, 2018-06-14 10:26
Normal topic InterfaceAnalyzer：“too many tries in fill_missing_atoms!”
by mxp » Tue, 2019-08-06 00:41 		8
 7,327 by mxp
Mon, 2019-08-12 18:42
Normal topic [SOLVED]core.io.silent: [ WARNING ] ...
by fred » Wed, 2011-10-05 07:38 		8
 8,399 by fred
Mon, 2014-04-21 06:47
Normal topic Syntax to build a silent file
by lanselibai » Fri, 2014-09-26 09:13 		8
 10,321 by lanselibai
Tue, 2014-09-30 03:45
Normal topic demo of molecular replacement with rosetta (mr_rosetta)
by wenchangyu2008 » Sun, 2011-03-20 05:23 		8
 11,558 by astrofunk12
Mon, 2014-04-21 06:47
Normal topic Noncanonical amino acids
by wsgosal » Tue, 2014-03-18 05:29 		8
 7,897 by e3lm
Thu, 2022-05-26 12:51
Normal topic fixbb design using damped LJ
by Anonymous » Fri, 2012-08-17 03:51 		8
 8,244 by Anonymous
Mon, 2014-04-21 06:47
Normal topic SnugDock - What protocol should I use?
by dfcoelho » Tue, 2018-11-27 07:32 		8
 7,894 by dfcoelho
Wed, 2018-11-28 08:07
Normal topic errors about RIFdocking
by sia » Sun, 2022-07-24 20:45 		8
 3,355 by Minghui-Du
Sun, 2024-03-24 21:12
Normal topic Problems with Ligand Docking
by saxen » Fri, 2011-08-19 00:19 		8
 9,179 by glemmon
Mon, 2014-04-21 06:47
Normal topic Adding bridged water interaction in constraint file
by purvi24 » Thu, 2019-02-28 07:01 		8
 5,656 by purvi24
Mon, 2019-03-11 06:43
Normal topic Fold tree C->N: RosettaScripts
by aroop » Wed, 2013-02-13 10:31 		8
 8,453 by smlewis
Mon, 2014-04-21 06:47
Normal topic Why do non proten ligands get a very high score in kinematic loop modeling/ in general?
by a_s_a » Wed, 2011-06-15 00:03 		8
 8,362 by a_s_a
Mon, 2014-04-21 06:47
Normal topic Converting -patch replonly residues to original sequence
by subha » Mon, 2017-06-26 13:39 		8
 6,489 by smlewis
Tue, 2017-07-04 15:42
Normal topic fix the left part doesn't work
by albumns » Wed, 2012-11-07 00:02 		9
 7,409 by albumns
Mon, 2014-04-21 06:47
Normal topic RosettaDock - Constraints File
by edpryor » Wed, 2012-09-19 06:23 		9
 13,114 by joeg
Mon, 2014-04-21 06:47
Normal topic how to fix the ATP HETATM by using movemap or constraint file?
by ziqi1234 » Mon, 2017-11-20 06:43 		9
 7,428 by ziqi1234
Wed, 2017-11-22 06:21
Normal topic Including waters in RosettaCM
by ajkal » Thu, 2017-04-27 11:59 		9
 8,092 by rpavlov
Tue, 2017-06-06 11:45
Normal topic ORBITAL records in self generated .params (ligands)
by ast » Thu, 2014-03-06 07:22 		9
 9,529 by ast
Thu, 2014-03-13 07:17
Normal topic Runnig Abinitio & score app
by Gaurav_kumar » Wed, 2011-11-23 20:45 		9
 12,054 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Symmetry Docking and Clustering with Ligands
by skovacs » Wed, 2012-03-07 16:46 		9
 12,078 by Anonymous
Mon, 2014-04-21 06:47
Normal topic RAbD with N-term，Proline-like ncaa returns segmentation fault during CCDEndsGraftMover
by CordycepsLin » Sun, 2022-02-06 19:09 		9
 4,028 by CordycepsLin
Wed, 2022-02-09 19:39
Normal topic problems in InterfaceAnalyzer analysis
by chenchaozhao » Fri, 2011-12-02 23:36 		9
 9,083 by smlewis
Mon, 2014-04-21 06:47
Normal topic ab initio membrane error (frag9 file...)
by almeida » Mon, 2012-07-30 08:53 		9
 9,937 by rmoretti
Tue, 2014-08-12 08:15
Normal topic Ab-initio peptide-protein docking
by suhail » Sun, 2013-06-23 16:20 		9
 12,407 by rmoretti
Fri, 2016-04-29 08:57
Normal topic cryptic error message from remodel in rosetta_scripts
by petrikigor » Mon, 2012-12-03 15:13 		9
 9,128 by petrikigor
Mon, 2014-04-21 06:47
Normal topic loop re-modeling std::out_of_range
by rlwoltz » Tue, 2013-03-12 18:11 		9
 9,246 by smlewis
Mon, 2014-04-21 06:47
Normal topic A problem with "molfile_to_params.py"
by Rosettasz » Mon, 2013-08-19 19:35 		10
 11,648 by egecav
Mon, 2021-01-18 05:41
Normal topic how to repacking loop while freezing other residues?
by jfhuang » Wed, 2012-07-25 06:59 		10
 9,194 by jfhuang
Mon, 2014-04-21 06:47
Normal topic Questions for "modeling_instructions.pdf" in "Homology or Loop Modelling"
by lanselibai » Sun, 2014-09-21 09:02 		10
 11,234 by lanselibai
Tue, 2014-10-07 02:58
Normal topic RosettaDNA error
by deltag » Fri, 2012-12-07 06:09 		10
 10,225 by deltag
Mon, 2014-04-21 06:47
Normal topic SEWING and motif file generation
by rbjacob » Thu, 2018-07-12 07:28 		10
 7,334 by zhangying1990
Tue, 2019-06-04 18:04
Normal topic std::bad_alloc error after changing .xml script?
by chrisHKL » Wed, 2020-03-04 11:44 		10
 6,036 by jadolfbr
Thu, 2020-03-05 07:02
Normal topic fixing disulfides in homolgy modeling
by pdbb » Wed, 2013-02-13 11:43 		10
 12,410 by kamau
Mon, 2014-09-22 09:39
Normal topic Don't know how to extract scores from a RNA de novo silent file.
by Basantab » Wed, 2011-11-23 17:27 		10
 10,419 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddg_monomer problem
by deltag » Wed, 2012-04-04 07:53 		11
 12,952 by smlewis
Mon, 2014-04-21 06:47
Normal topic Abinitio error: ERROR: Value of inactive option accessed: -in:file:frag9
by rlwoltz » Tue, 2012-09-18 14:04 		11
 16,873 by RAGHURAMAN
Fri, 2014-08-08 02:19
Normal topic Rosetta-Holes Scoring Function
by kroberts » Fri, 2011-05-13 14:05 		11
 15,336 by rmoretti
Mon, 2014-04-21 06:47
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
 11,036 by smlewis
Mon, 2014-04-21 06:47
Normal topic Should FastRelax be commented out in Calculate_protein_protein_ddg demo?
by cossio » Mon, 2016-10-31 12:01 		11
 9,967 by cossio
Mon, 2016-11-21 07:56
Normal topic XML validation failing
by mb0261 » Fri, 2023-04-14 14:53 		11
 2,744 by mb0261
Mon, 2023-04-17 17:38
Normal topic fragment_picker.mpi.linuxgccrelease can't find : libsqlite3.so
by starone » Mon, 2016-06-20 19:22 		11
 14,100 by starone
Fri, 2016-06-24 18:29
Normal topic Error while running Enzyme Design
by saxen » Fri, 2011-10-21 15:46 		11
 11,506 by akpole
Mon, 2014-04-21 06:47
Normal topic Where is the RosettaHoles2 executable?
by lah435 » Mon, 2012-06-04 15:15 		11
 9,152 by smlewis
Mon, 2014-04-21 06:47
Normal topic No output pdb files after docking protein and DNA/RNA
by yzq » Thu, 2012-10-25 08:23 		11
 12,589 by rmoretti
Fri, 2016-06-17 10:22
Normal topic in silico affinity maturation design
by jarod » Mon, 2013-05-20 02:07 		11
 12,953 by jarod
Mon, 2014-04-21 06:47
Normal topic -kill_hairpin error
by jadolfbr » Wed, 2011-10-05 18:53 		11
 18,071 by rmoretti
Mon, 2015-09-28 15:00
Normal topic fragment picker does not follow dihedral constraints
by attesor » Tue, 2016-05-24 23:22 		12
 11,371 by smlewis
Wed, 2016-08-17 07:56
Normal topic AbinitioRelax usage (3.4)
by atruong » Fri, 2012-10-12 13:38 		12
 11,680 by atruong
Mon, 2014-04-21 06:47
Normal topic Scoring residue vs. organic ligand
by almeida » Tue, 2014-04-08 12:18 		12
 14,202 by rmoretti
Thu, 2014-04-24 14:43
Normal topic Surface Docking Application Crash
by dkozuch » Sat, 2017-09-02 18:32 		12
 9,234 by Anpu
Tue, 2018-09-25 19:06
Normal topic "score vs RMSD plots" & "cluster models"
by lanselibai » Thu, 2014-09-25 06:51 		12
 25,604 by lanselibai
Wed, 2014-10-15 01:54