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Rosetta 3 - General

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Normal topic keep ATP in the kinase-peptide structure while docking
by ziqi1234 » Fri, 2017-11-10 04:04
0
947 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic Cannot Open Resfile
by csvajda » Fri, 2022-03-04 13:39
3
948 by csvajda
Mon, 2022-03-07 07:46
Normal topic Error: Start tag expected, '<' not found
by Isomerase » Wed, 2022-04-06 19:45
1
948 by rmoretti
Thu, 2022-04-07 07:51
Normal topic Sequence Profile/Checkpoint file
by ojmel » Fri, 2021-04-02 17:29
1
948 by taylorjones
Mon, 2021-04-05 13:17
Normal topic What is the expected behaviour when minimizing a jump edge?
by bio_james » Wed, 2017-12-13 09:13
0
950 by bio_james
Wed, 2017-12-13 09:13
Normal topic Help deciphering an input
by Elijah_Hix » Wed, 2021-09-22 11:12
2
951 by Elijah_Hix
Thu, 2021-09-23 10:13
Normal topic Docking Metalloprotein-Protein
by fgomes » Fri, 2019-11-22 19:12
0
957 by fgomes
Fri, 2019-11-22 19:12
Normal topic alignblast.pl truncated file
by rlwoltz » Mon, 2019-03-11 18:32
0
963 by rlwoltz
Mon, 2019-03-11 18:32
Normal topic Method to keep ATP in the certain position in the prepack step
by ziqi1234 » Tue, 2017-11-21 05:55
0
971 by ziqi1234
Tue, 2017-11-21 05:55
Normal topic Errors in Interface_design_demo
by zhoubin » Fri, 2019-01-04 13:14
0
976 by zhoubin
Fri, 2019-01-04 13:14
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53
0
980 by ela
Fri, 2018-08-31 02:53
Normal topic opencl support programs
by x_wuxi » Mon, 2021-04-12 18:17
1
985 by rmoretti
Tue, 2021-04-13 06:42
Normal topic error when using script best_ifaceE.py
by windmill » Thu, 2020-06-18 21:30
1
987 by windmill
Thu, 2020-06-18 21:32
Normal topic Differentiable Energy Function w/ Centroid Representation
by protein_fan » Sun, 2022-03-20 09:39
4
992 by protein_fan
Fri, 2022-04-15 17:41
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
1,008 by patcD
Wed, 2021-09-01 06:54
Normal topic Recommendations for CoupledMoves enzyme redesign
by dgm3 » Thu, 2021-03-04 10:53
1
1,011 by aloshbau
Tue, 2021-03-09 02:47
Normal topic Disulfidize mover
by karenjgonzalez » Wed, 2019-07-31 12:35
0
1,013 by karenjgonzalez
Wed, 2019-07-31 12:35
Normal topic partial charge of params file in ligand docking
by rohi » Fri, 2021-05-28 08:43
1
1,018 by rmoretti
Fri, 2021-05-28 08:54
Normal topic Chain name being read as residue
by MarkusAurelius » Mon, 2021-03-22 11:19
2
1,046 by MarkusAurelius
Mon, 2021-03-29 09:06
Normal topic solution of the length of peptide candidates is larger than substrate with FlexPepDock and Flexpepbind
by ziqi1234 » Thu, 2018-05-24 02:18
0
1,055 by ziqi1234
Thu, 2018-05-24 02:18
Normal topic enzyme design implementation
by rohi » Wed, 2020-12-16 09:54
1
1,056 by rmoretti
Tue, 2021-02-09 11:30
Normal topic protein design for increasing its affinity towards ligand
by rohi » Fri, 2020-10-30 11:33
1
1,061 by rmoretti
Tue, 2021-02-09 12:25
Normal topic Problem with undetected lower and upper terminus variants for new polymer
by Martin Floor » Sat, 2022-06-11 06:51
5
1,065 by matteoferla
Fri, 2022-07-01 13:49
Normal topic loop modelling on complex structure
by Tianyang89 » Fri, 2020-09-18 07:24
1
1,068 by amelie.stein
Mon, 2020-09-28 10:41
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
1,074 by sheehajh
Fri, 2020-02-21 12:41
Normal topic reading of AtomPair failed in relax with constraint
by hajar » Wed, 2020-06-10 10:02
0
1,075 by hajar
Wed, 2020-06-10 11:17
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39
2
1,075 by almeida85
Mon, 2021-02-08 09:50
Normal topic I Need Help on Validation for a Ligand Docking Experiment.
by tbelec » Sat, 2021-03-20 13:27
1
1,077 by matteoferla
Mon, 2021-03-22 08:29
Normal topic Fragment Picker score type weights
by wellsm10 » Mon, 2020-12-14 13:05
1
1,078 by dgront
Thu, 2021-02-11 08:30
Normal topic simple_cycpep_predict issue modifying terminal residue
by JEaston » Thu, 2020-06-25 13:15
1
1,080 by vmulligan
Mon, 2020-06-29 13:09
Normal topic FastRelax Mover with symmetry, ligand and membrane
by Michele.Bonus » Wed, 2021-05-26 04:43
1
1,081 by matteoferla
Thu, 2021-06-03 08:24
Normal topic Speeding up FastDesign
by ebetica0 » Wed, 2021-04-28 13:08
1
1,082 by vmulligan
Wed, 2021-04-28 14:20
Normal topic PIPER-FlexPepDock protocol file apply_ftresult.py missing
by diasmarieli » Thu, 2021-11-04 06:33
2
1,087 by diasmarieli
Fri, 2021-11-26 05:11
Normal topic Score function: unable to open input_files/1qys.pdb
by Cyrrusm » Tue, 2020-10-13 11:35
1
1,088 by rmoretti
Tue, 2020-10-13 11:40
Normal topic constraint are not imposed during protein-ligand docking
by rohi » Wed, 2020-12-02 11:28
1
1,090 by rmoretti
Tue, 2021-02-09 12:02
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
1,091 by matteoferla
Wed, 2020-01-01 04:30
Normal topic use_truncated_termini not working in combination with params files
by georg » Thu, 2020-03-26 13:14
1
1,094 by matteoferla
Tue, 2020-04-14 03:36
Normal topic Why does the sum of the per-residue total energy not match the whole score?
by matteoferla » Fri, 2021-07-09 08:36
2
1,094 by matteoferla
Mon, 2021-07-12 02:23
Normal topic Help with filtering (Rosetta scripts)
by wentlewi » Sat, 2020-10-24 10:12
1
1,095 by rmoretti
Tue, 2021-02-09 12:35
Normal topic Rosetta Double changing mmCIF chain ID
by Victor Tobiasson » Thu, 2021-05-13 07:57
2
1,095 by Victor Tobiasson
Thu, 2021-05-13 08:33
Normal topic lDDT: local Distance Difference Test implemented?
by ipetrik_ambry » Wed, 2017-12-06 13:11
0
1,097 by ipetrik_ambry
Wed, 2017-12-06 13:11
Normal topic RifDock building error on Ubuntu 20.04,please help!
by guowuchen » Mon, 2022-03-28 03:53
2
1,098 by guowuchen
Wed, 2022-03-30 04:20
Normal topic Gaussian Constraint For Dihedrals
by jinli711 » Thu, 2020-07-23 10:47
1
1,101 by matteoferla
Fri, 2020-07-24 03:06
Normal topic Error in Hybridize of Rosetta Comparative Modeling.
by Ivan » Fri, 2019-11-01 07:46
1
1,102 by rmoretti
Mon, 2019-11-04 12:54
Normal topic clustering ligand binding mood by ligand RMSD
by rohi » Tue, 2021-01-26 21:11
1
1,102 by brownbp1
Tue, 2021-02-09 12:12
Normal topic Ligand docking: how to generate the crystal_complex.pdb with hydrogens added
by nhinguyen26 » Wed, 2020-06-17 15:03
1
1,104 by matteoferla
Sat, 2020-06-20 03:56
Normal topic Running CstFileToTheozyme for Mono-Atomic Metal
by Jhreed » Fri, 2016-07-08 13:43
0
1,113 by Jhreed
Fri, 2016-07-08 13:44
Normal topic Setting output values using a database (with relax app)
by pedro.guillem » Thu, 2020-05-14 04:33
1
1,118 by pedro.guillem
Wed, 2020-06-24 04:41
Normal topic There is a problem executing “rosetta_scripts.static.linuxgccrelease ”
by zjya » Tue, 2021-02-02 23:44
1
1,120 by rmoretti
Wed, 2021-02-03 14:45
Normal topic Rosetta-foldtree and docking
by tingting » Tue, 2022-03-15 22:49
5
1,129 by aastha.pal
Mon, 2022-06-27 09:55
Normal topic Error using FilterScan with rosettascripts
by SenyorDrew » Tue, 2016-12-13 14:29
0
1,135 by SenyorDrew
Tue, 2016-12-13 14:29
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42
3
1,137 by rmoretti
Tue, 2023-05-09 15:32
Normal topic Unable to create col_complex.pdb file
by sayan500 » Tue, 2019-07-30 22:08
1
1,140 by rmoretti
Mon, 2019-08-26 14:52
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
1,145 by rmoretti
Tue, 2019-07-09 15:59
Normal topic Error in src/protocols/membrane/util.cc line: 1224
by renedominik » Tue, 2020-02-11 08:10
1
1,148 by renedominik
Wed, 2020-02-12 06:16
Normal topic error running "helix_preassemble_setup.py"
by zahra_AZ » Tue, 2020-11-03 01:54
1
1,149 by rmoretti
Tue, 2021-02-09 12:19
Normal topic File specification of binary part of silent file (especially PDB section)
by m.ebert » Wed, 2019-05-29 01:52
1
1,157 by smlewis
Wed, 2019-05-29 13:21
Normal topic problem plotting results from docking_analyser with provided Rscript
by madammolecular » Mon, 2021-02-01 14:44
2
1,159 by amystevens
Thu, 2021-09-30 14:18
Normal topic Is there other online server for generate fragment?
by ylwang » Wed, 2020-04-01 01:39
1
1,168 by rmoretti
Wed, 2020-04-01 10:10
Normal topic Structure-sequence alignment generation with selected PDB how?
by nzsuzsanna » Tue, 2016-05-10 07:39
0
1,169 by nzsuzsanna
Tue, 2016-05-10 07:39
Normal topic computing Pnear for Rosetta ligand docking
by rohi » Mon, 2021-02-01 08:27
1
1,185 by rmoretti
Tue, 2021-02-09 09:37
Normal topic Denovo prediction from multiple fragment lengths
by ahmadkhalifa » Sun, 2019-03-24 03:55
1
1,186 by rmoretti
Sat, 2019-03-30 12:10
Normal topic de novo protein prediction
by pci112 » Tue, 2021-03-23 10:13
2
1,187 by pci112
Thu, 2021-03-25 01:44
Normal topic Error in flex ddG tutorial
by wentlewi » Sat, 2020-05-16 08:06
0
1,189 by wentlewi
Sat, 2020-05-16 08:06
Normal topic Molfile to Params File Issue
by jferrie » Mon, 2018-04-23 15:25
0
1,192 by jferrie
Mon, 2018-04-23 15:25
Normal topic Mutations are ignored (fixbb) when using -auto_setup_metals option
by hdelrisco » Wed, 2019-06-19 15:43
1
1,194 by smlewis
Fri, 2019-06-28 13:56
Normal topic Rosetta changing Atom Name in PDB ATOM record?
by chrisHKL » Tue, 2020-03-03 20:50
1
1,195 by smlewis
Wed, 2020-03-04 07:40
Normal topic pyrosetta.rosetta.core.pose.rna
by chenjief » Tue, 2021-11-23 07:03
3
1,207 by matteoferla
Mon, 2022-01-10 06:44
Normal topic problems with implementing NOE constraints
by connyyu » Thu, 2019-04-11 12:37
1
1,210 by connyyu
Thu, 2019-04-18 03:26
Normal topic Ligand being read as part of protein structure
by MarkusAurelius » Thu, 2021-04-01 11:00
2
1,210 by MarkusAurelius
Fri, 2021-04-02 11:44
Normal topic Helical symmetry for cryo-EM refinement
by fmerino » Mon, 2017-10-16 04:02
0
1,220 by fmerino
Mon, 2017-10-16 04:02
Normal topic Rosetta Antibody cuts off light chain?
by ziheng@mit.edu » Thu, 2019-05-02 15:17
1
1,221 by jeliazkov
Fri, 2019-05-03 07:00
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
1,227 by rmoretti
Wed, 2019-09-18 10:49
Normal topic Rosetta params for taxol
by ahmadkhalifa » Sat, 2019-03-30 22:37
1
1,230 by rmoretti
Wed, 2019-04-03 10:03
Normal topic Ligand question - aromatic bonds not being enforced?
by Rick_Baker » Wed, 2019-09-11 09:08
1
1,234 by Rick_Baker
Wed, 2019-09-11 15:35
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09
3
1,234 by matteoferla
Fri, 2021-08-20 08:37
Normal topic running Rosetta with MPI
by rohi » Sat, 2020-09-05 16:06
1
1,244 by rmoretti
Tue, 2021-02-09 13:44
Normal topic mpi + mp_mutate_relax
by decrSTL » Thu, 2020-01-16 10:47
1
1,245 by jkleman
Thu, 2020-01-16 11:05
Normal topic Params file for Methane
by dasdevashishdas » Sun, 2018-10-07 21:34
1
1,261 by rmoretti
Mon, 2018-10-08 11:20
Normal topic Constraints use in RosettaCM
by a.book » Wed, 2018-10-03 12:11
0
1,267 by a.book
Wed, 2018-10-03 15:56
Normal topic MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"
by dfcoelho » Mon, 2020-02-03 11:09
1
1,269 by dfcoelho
Tue, 2020-02-04 07:45
Normal topic RosettaRemodel gives no increased output when setting higher -num_trajectory
by JW_24 » Tue, 2020-09-22 11:49
2
1,270 by JW_24
Wed, 2020-09-23 01:27
Normal topic MakeRotLib
by yinasun » Sun, 2019-07-28 20:08
1
1,271 by rmoretti
Mon, 2019-08-26 15:00
Normal topic How to specify a specific rotamer
by Lior_UCSF » Wed, 2018-02-21 20:35
1
1,272 by rmoretti
Thu, 2018-02-22 09:29
Normal topic intrensic disrodered proteins
by ac.research » Thu, 2019-04-04 07:20
1
1,273 by vmulligan
Mon, 2019-04-08 14:49
Normal topic AbinitioRelax of RCSB PDB structures
by ac.research » Tue, 2019-09-03 02:35
1
1,273 by danpf
Tue, 2019-09-03 10:39
Normal topic Relax output mmCIF file to a particular path
by AJVincelli » Sun, 2018-11-25 11:04
1
1,274 by AJVincelli
Sun, 2018-11-25 11:09
Normal topic Questions regarding fragmentation using Robetta
by ahmadkhalifa » Thu, 2018-06-28 13:24
1
1,278 by smlewis
Thu, 2018-06-28 13:34
Normal topic patch file modification for ser_phosphorylated.txt
by hajar » Sun, 2020-06-21 00:49
1
1,278 by matteoferla
Tue, 2020-06-23 10:58
Normal topic Issues with angle Constraints during Docking
by LeonhardJS » Thu, 2021-01-28 04:40
2
1,287 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic cluster results
by albumns » Sun, 2010-07-18 23:59
0
1,290 by albumns
Mon, 2014-04-21 06:47
Normal topic ref2015: approx. kcal/mol or actually kJ/mol?
by matteoferla » Thu, 2021-10-07 04:04
2
1,290 by matteoferla
Thu, 2021-10-07 09:31
Normal topic Docking a ligand to two movable domains of a protein
by brspurri » Wed, 2018-05-16 08:27
1
1,291 by rmoretti
Thu, 2018-06-28 14:22
Normal topic possible error in make_fragments.pl and fix
by DanielK » Fri, 2012-04-27 02:21
0
1,293 by DanielK
Mon, 2014-04-21 06:47
Normal topic Problem with the top 25 fragments used in the library of 200 nine-residue fragments in AbinitioRelax
by MA » Wed, 2017-07-26 01:12
1
1,293 by rmoretti
Mon, 2017-08-21 09:55
Closed topic MakeRotLib
by yinasun » Fri, 2019-07-26 02:20
1
1,297 by rmoretti
Mon, 2019-08-26 15:01
Normal topic Error in Loop Modeling
by sayan500 » Tue, 2019-07-30 22:20
0
1,298 by sayan500
Tue, 2019-07-30 22:20
Normal topic IS there any source code about protein structure prediction with only sequences information?
by ylwang » Mon, 2019-07-08 02:36
1
1,311 by rmoretti
Mon, 2019-07-08 08:05
Normal topic distance contraints file
by tricia » Wed, 2009-06-10 13:28
0
1,311 by tricia
Mon, 2014-04-21 06:47
Normal topic How to extract antibody from a set of pdb file may may contain antigen?
by Sunyp_IM » Mon, 2017-11-13 17:11
1
1,319 by ac.research
Sat, 2017-11-18 06:54
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