This historical page is locked! For new posts see Github Discussions.

You are here

Home » Forums » Rosetta 3

Rosetta 3 - General

Topic / Topic starter Replies Viewssort descending Last post
Normal topic Is the packer aware of non canonical amino acids?
by krdav » Tue, 2016-08-16 08:16 		7
 6,765 by krdav
Wed, 2016-08-17 12:57
Normal topic loop remodelling with a fixed bound DNA
by jtmacd » Thu, 2010-02-25 03:23 		8
 6,788 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Problem with clustering 1000 centroid pdbs
by doranhen » Sat, 2012-04-28 10:34 		6
 6,806 by doranhen
Mon, 2014-04-21 06:47
Normal topic Using 2 non-standard residues in one run
by einew » Tue, 2011-03-08 21:24 		5
 6,830 by einew
Mon, 2014-04-21 06:47
Normal topic first try at relaxing a structure
by einew » Wed, 2011-01-05 11:09 		4
 6,844 by einew
Mon, 2014-04-21 06:47
Normal topic optH flag makes hydrogen bond energy scores worse...
by tsjain » Fri, 2012-07-13 14:04 		6
 6,864 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to use AbinitioRelax.mpi.linuxgccrelease?
by albumns » Mon, 2012-03-26 22:50 		5
 6,866 by smlewis
Mon, 2014-04-21 06:47
Normal topic About align hundreds of pdb structures produced by rosseta membrane abinitio
by ritacc18 » Wed, 2013-05-22 12:37 		5
 6,893 by ssrb
Tue, 2015-09-22 08:35
Normal topic P-P docking with ambiguous constraints
by Anouk » Fri, 2013-11-08 11:38 		5
 6,904 by rmoretti
Mon, 2014-04-21 06:48
Normal topic best_ifaceE.py error
by rosa » Fri, 2013-07-12 08:35 		7
 6,979 by rosa
Mon, 2014-04-21 06:48
Normal topic SASA packing score in Rosetta 3.1
by enoee » Wed, 2010-07-28 01:45 		6
 6,996 by smlewis
Mon, 2014-04-21 06:47
Normal topic Structure refinement guided by Cryo-EM density maps
by ahmadkhalifa » Thu, 2018-03-08 08:22 		7
 7,057 by ahmadkhalifa
Tue, 2018-05-01 09:04
Normal topic Loop Modeling Deletes Residues
by Julix » Wed, 2012-09-05 10:14 		7
 7,076 by smlewis
Mon, 2014-04-21 06:47
Normal topic Question on eval_atom_derivative function.
by Al52 » Thu, 2015-12-03 16:17 		7
 7,086 by rmoretti
Thu, 2016-02-04 09:29
Normal topic I am a beginner in rosetta software and need help to build params file
by nais » Fri, 2011-03-18 13:37 		3
 7,088 by rmoretti
Mon, 2014-04-21 06:47
Normal topic mitochondria protein modeling
by rlwoltz » Fri, 2012-10-26 14:32 		6
 7,111 by smlewis
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
 7,153 by Anonymous
Mon, 2014-04-21 06:47
Normal topic What is a "silent file"?
by lanselibai » Mon, 2014-09-22 02:43 		2
 7,206 by lanselibai
Mon, 2014-09-22 08:13
Normal topic defining interface in interface analyzer
by aa20 » Fri, 2013-09-27 11:08 		5
 7,226 by smlewis
Mon, 2014-04-21 06:48
Normal topic log files
by shadrinams » Fri, 2018-01-26 07:29 		7
 7,227 by shadrinams
Mon, 2018-02-12 11:47
Normal topic rerun same experiment on MPI.
by exchhattu » Tue, 2010-02-23 21:14 		7
 7,259 by exchhattu
Mon, 2014-04-21 06:47
Normal topic cluster pdb structures questions
by ritacc18 » Thu, 2013-03-28 19:20 		5
 7,298 by ritacc18
Mon, 2014-04-21 06:47
Normal topic How to define specific residues in alascan ?
by Park » Mon, 2011-06-13 19:56 		6
 7,349 by smlewis
Mon, 2014-04-21 06:47
Normal topic What's a good application to thread a sequence over a peptide (of a peptide-protein complex) and minimize?
by brspurri » Tue, 2013-02-12 08:19 		6
 7,377 by smlewis
Mon, 2014-04-21 06:47
Normal topic pdb files in Rosetta format
by zhisheng » Mon, 2011-10-31 08:52 		6
 7,463 by smlewis
Mon, 2014-04-21 06:47
Normal topic Energy calculation for protein design
by Filipe » Sat, 2011-11-26 15:01 		4
 7,529 by Filipe
Mon, 2014-04-21 06:47
Normal topic Cannot run binaries after successful compilation
by ac.research » Mon, 2017-08-14 02:56 		6
 7,562 by ac.research
Fri, 2017-08-18 00:57
Normal topic A question about Multiple constraints
by kxiao » Mon, 2014-06-16 07:02 		7
 7,571 by masterofpuppets
Fri, 2014-12-19 08:30
Normal topic Reproducing Rosetta++ scoring function with Rosetta 3?
by JuliusSu » Mon, 2014-03-17 21:15 		7
 7,573 by JuliusSu
Wed, 2014-03-19 20:38
Normal topic extraction of pdbs from silent.out files on Mac
by pramod » Tue, 2014-01-07 11:43 		5
 7,585 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Error with non-canonical amino acid in SnugDock.
by sk0319 » Thu, 2016-12-29 16:12 		8
 7,631 by sk0319
Wed, 2017-01-11 10:52
Normal topic Error_fragment_generation
by Payal Chatterjee » Fri, 2016-02-12 12:11 		6
 7,648 by G Mustafa
Fri, 2021-09-10 01:16
Normal topic Using rosetta 3 to make a fragment library and then use it to model loop of a protein structure
by bharat_46010 » Sun, 2011-01-23 05:22 		4
 7,683 by dgront
Mon, 2014-04-21 06:47
Normal topic This element is not expected.
by ac.research » Fri, 2017-10-13 03:47 		6
 7,736 by vmulligan
Thu, 2020-07-16 23:31
Normal topic building a 77 aa long protein fragment
by tevang » Sat, 2010-02-20 11:37 		8
 7,770 by gsmurphy
Mon, 2014-04-21 06:47
Normal topic Fe3p Heme Iron Unrecognized Despite Loading Hem Params
by vsjasion » Fri, 2011-09-02 10:37 		6
 7,813 by tigerous
Mon, 2014-04-21 06:47
Normal topic AbinitioRelax under different directories without -constant_seed -jran flag
by xpzhang » Wed, 2010-09-15 14:56 		6
 7,819 by rmoretti
Mon, 2014-04-21 06:47
Normal topic cutpoint error!
by monos_morpheus » Thu, 2011-04-07 08:04 		7
 7,953 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic Rosetta3 Tutorials Beta Release
by smlewis » Fri, 2011-08-19 13:35 		7
 7,966 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaVIP
by nick.polizzi » Tue, 2013-08-06 15:13 		8
 7,992 by rmoretti
Mon, 2014-04-21 06:48
Normal topic errors while running rosetta 3.1
by isengupta13 » Tue, 2011-05-17 18:11 		7
 8,025 by jurkm
Mon, 2014-04-21 06:47
Normal topic uninstalling or rebuilding rosetta
by rlwoltz » Thu, 2013-04-11 11:45 		5
 8,052 by rlwoltz
Mon, 2014-04-21 06:47
Normal topic Interface rmsd calculation Irms
by mahajanr » Wed, 2010-07-07 18:24 		5
 8,063 by mahajanr
Mon, 2014-04-21 06:47
Normal topic ERROR: Unable to open weights/patch file
by peony » Sun, 2013-11-17 02:49 		4
 8,073 by rmoretti
Tue, 2019-07-09 10:29
Normal topic modeling residues with covalent ligand attachments
by sid » Fri, 2011-04-15 09:16 		5
 8,103 by rmoretti
Fri, 2015-07-03 14:02
Normal topic Error running Abinitio relax with @flags
by samuelrpita » Mon, 2015-10-05 13:20 		7
 8,184 by rmoretti
Tue, 2015-10-27 09:11
Normal topic Rosetta3.3 enzyme_design errors
by jtmacd » Wed, 2012-01-25 03:33 		7
 8,216 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaDock decoys recoring with ZRANK
by cheyuk » Fri, 2014-04-11 01:40 		5
 8,225 by rmoretti
Thu, 2016-04-28 15:53
Normal topic Every thing Ok in PC end Error on Server
by jrcf » Tue, 2016-03-22 07:21 		8
 8,267 by jrcf
Wed, 2016-03-23 12:16
Normal topic Relax structure using Membrane Environment Scoring Function
by anna.duncan » Thu, 2010-02-04 08:01 		6
 8,275 by jruhym
Mon, 2014-04-21 06:47
Normal topic how to transfer the rosetta score to physical unit?
by Lindsay » Thu, 2012-06-28 09:33 		7
 8,280 by Lindsay
Mon, 2014-04-21 06:47
Normal topic ab inito memberane error
by albumns » Mon, 2011-02-14 10:58 		5
 8,288 by albumns
Mon, 2014-04-21 06:47
Normal topic Relax Refinement for complecated targets
by jiongzhang » Fri, 2012-01-20 09:57 		10
 8,426 by jiongzhang
Mon, 2014-04-21 06:47
Normal topic The design of a helical peptide
by Jacob-kong » Tue, 2012-06-26 06:26 		6
 8,438 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic Using Patches in Rosetta
by JS » Wed, 2010-03-10 13:32 		6
 8,440 by JS
Mon, 2014-04-21 06:47
Normal topic type of docking
by rohi » Mon, 2020-07-06 06:55 		11
 8,506 by rohi
Sun, 2020-07-26 17:03
Normal topic is it possible to generate models without hydrogen?
by albumns » Fri, 2012-03-02 12:24 		9
 8,553 by albumns
Mon, 2014-04-21 06:47
Normal topic Looking for a pdb....
by MarkW » Mon, 2014-10-13 15:45 		8
 8,564 by rmoretti
Mon, 2014-11-03 16:30
Normal topic kinematic loop modeling/sequence design keeps crashing with segmentation fault
by banshee » Thu, 2013-03-28 09:52 		8
 8,598 by smlewis
Mon, 2014-04-21 06:47
Normal topic Debugging Rosetta under XCode
by sacch » Sun, 2011-10-16 18:23 		8
 8,632 by sacch
Mon, 2014-04-21 06:47
Normal topic ERROR: Unused "free" argument specified: GDP.fa.tors
by ahmadkhalifa » Fri, 2018-06-15 11:27 		10
 8,678 by smlewis
Tue, 2018-06-19 09:28
Normal topic Docking + Active Site Design
by bharat_46010 » Sat, 2014-12-13 23:04 		7
 8,743 by rmoretti
Wed, 2015-01-21 08:43
Normal topic What is the general protocol for antibody-antigen docking without the native antibody-antigen structures?
by Sunyp_IM » Sun, 2017-08-13 05:42 		11
 8,747 by smlewis
Tue, 2017-08-29 08:56
Normal topic Using D-amino acids in Rosetta docking
by moehle » Wed, 2011-06-01 00:49 		7
 8,804 by moehle
Mon, 2014-04-21 06:47
Normal topic De novo Protein Design
by ac.research » Sat, 2017-07-15 10:39 		5
 8,894 by rmoretti
Mon, 2017-08-14 09:06
Normal topic Clustering using an disrupted run silent file
by PaulaBanks » Mon, 2013-07-15 02:19 		9
 8,911 by rmoretti
Wed, 2014-09-24 09:57
Normal topic Loop Modeling with fixed backbone
by bharat_46010 » Mon, 2011-12-19 05:20 		9
 8,957 by bharat_46010
Mon, 2014-04-21 06:47
Normal topic using constraints with AbinitioRelax (Rosetta 3.1)
by ndousis » Fri, 2009-12-18 08:56 		8
 8,966 by ndousis
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer packstat score = 0.000
by vmc99 » Fri, 2018-11-16 11:30 		11
 9,009 by SenyorDrew
Wed, 2019-06-12 14:10
Normal topic side-chain refinement
by qlj » Wed, 2013-02-20 04:40 		6
 9,025 by qlj
Mon, 2014-04-21 06:47
Normal topic Docking double-stranded DNA to a protein
by xpzhang » Tue, 2012-01-31 12:35 		5
 9,042 by xpzhang
Mon, 2014-04-21 06:47
Normal topic Talaris score function
by nawsad » Tue, 2013-05-21 03:32 		7
 9,122 by rmoretti
Mon, 2014-04-21 06:47
Normal topic pNNMAKE compilation
by adva » Sun, 2012-12-02 03:59 		10
 9,141 by smlewis
Mon, 2014-04-21 06:47
Normal topic ERROR READING PDB FILE
by asmi » Sat, 2011-02-26 07:23 		7
 9,168 by smlewis
Mon, 2014-04-21 06:47
Normal topic Resfile
by vijayaraj81 » Thu, 2014-02-27 01:14 		8
 9,202 by vijayaraj81
Tue, 2014-03-04 05:07
Normal topic Help with get_pdb.py for PDB file cleaning
by lzx32 » Mon, 2011-03-28 02:11 		7
 9,241 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problems with "pdb_renumber.py" in tutorial Advanced Protein-Protein Docking
by Sunyp_IM » Sun, 2017-06-25 02:40 		9
 9,312 by ac.research
Mon, 2018-05-14 10:20
Normal topic acceptable RMSD value in the clustered structures?
by ritacc18 » Wed, 2013-06-19 14:53 		3
 9,317 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Re: Protein-RNA interface design
by bharat_46010 » Tue, 2015-04-07 04:44 		9
 9,388 by rmoretti
Mon, 2015-06-01 15:27
Normal topic ERROR: Assertion Fdensity.u2 and Fdensity.u3 failed
by ahmadkhalifa » Wed, 2017-12-06 07:38 		13
 9,411 by brandon.frenz
Thu, 2018-03-08 09:28
Normal topic input_score_filter not taken by program cluster ?
by Anonymous » Mon, 2012-06-11 09:14 		9
 9,435 by attesor
Fri, 2014-10-31 04:49
Normal topic hydrophobicity patch
by Lindsay » Fri, 2012-05-04 08:24 		7
 9,481 by Lindsay
Mon, 2014-04-21 06:47
Normal topic what is "-relax:sequence" ?
by Anonymous » Fri, 2012-06-08 06:31 		10
 9,520 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to get multiple chains in PDB from Fold and Dock
by arthuc01 » Tue, 2012-05-29 02:05 		9
 9,535 by arthuc01
Mon, 2014-04-21 06:47
Normal topic Error when renumbering PDB
by dzhao » Wed, 2012-07-18 01:03 		7
 9,590 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13 		7
 9,595 by smlewis
Mon, 2014-04-21 06:47
Normal topic Remote access to Rosetta on Blue Gene or another HPC system?
by rfieldhouse » Mon, 2011-05-16 08:40 		10
 9,635 by rfieldhouse
Mon, 2014-04-21 06:47
Normal topic error during docking
by zhisheng » Thu, 2012-02-02 12:10 		10
 9,635 by smlewis
Mon, 2014-04-21 06:47
Normal topic Can Fold-and-dock protocol applied to membrane proteins
by justin » Thu, 2011-07-21 00:14 		9
 9,640 by wangyr
Mon, 2014-04-21 06:47
Normal topic Rosetta reference energy
by Lindsay » Mon, 2012-05-07 07:56 		9
 9,765 by Lindsay
Mon, 2014-04-21 06:47
Normal topic B1_SampleSegment1.sh from RosettaES tutorial crashes
by ab » Tue, 2017-07-04 08:42 		12
 9,831 by brandon.frenz
Sat, 2017-07-08 13:49
Normal topic AbinitioRelax with very small peptides
by jamsmad » Tue, 2012-09-04 13:45 		9
 9,841 by jamsmad
Mon, 2014-04-21 06:47
Normal topic Is it possible to do Abinitio folding from a linear structure.?
by monos_morpheus » Sat, 2011-04-16 09:13 		11
 9,865 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic what is minirosetta
by Lindsay » Tue, 2012-04-10 07:48 		2
 9,981 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Does the fold count reset if abinitio is restarted?
by burkheadlab » Mon, 2011-06-13 11:39 		10
 10,087 by rmoretti
Thu, 2017-02-02 08:32
Normal topic How to run Rosetta3 in parallel
by lennylv » Mon, 2009-03-30 04:21 		6
 10,096 by rmoretti
Mon, 2014-04-21 06:47
Normal topic memory issue rosetta3.4 scripts
by ast » Mon, 2013-01-28 06:25 		8
 10,177 by smlewis
Mon, 2014-04-21 06:47
Normal topic relax structure before design?
by Lindsay » Tue, 2013-11-05 20:50 		7
 10,239 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Submitting job to local cluster
by tusharranjanmoharana » Fri, 2016-04-15 01:38 		8
 10,313 by rmoretti
Mon, 2016-05-09 09:23
Normal topic How do you implement phosphoserine in ab -initio folding?
by smiruthi » Fri, 2011-12-16 14:45 		10
 10,348 by brspurri
Mon, 2014-04-21 06:47