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Rosetta 3 - General

Topic / Topic starter Repliessort descending Views Last post
Normal topic Questions about rosetta fragment library ranking and fragment conformation sampling algorithm
by mdyini » Thu, 2011-05-19 17:34 		3
 4,662 by dgront
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06 		3
 3,389 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic # decoys of silent
by fred » Wed, 2014-04-02 06:00 		3
 3,635 by fred
Fri, 2014-04-04 11:34
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09 		3
 2,024 by matteoferla
Fri, 2021-08-20 08:37
Normal topic Hbond tripped
by alejandro » Mon, 2011-11-21 04:17 		3
 3,920 by alejandro
Mon, 2014-04-21 06:47
Normal topic RosettaDock-4.0 score term
by Zjq1998 » Wed, 2022-06-29 22:07 		3
 1,694 by ssrb
Tue, 2022-07-05 11:07
Normal topic Error Scoring Application- Illegal attempt to score
by samuelrpita » Thu, 2015-08-06 14:45 		3
 5,125 by rmoretti
Wed, 2015-08-12 15:03
Normal topic core.scoring.rms_util: WARNING: CA_rmsd out of range...
by mdyini » Sat, 2012-02-25 16:14 		4
 4,486 by mdyini
Mon, 2014-04-21 06:47
Normal topic how to do cluster after low resolution protein-protein docking?
by albumns » Sat, 2010-11-27 01:17 		4
 4,600 by albumns
Mon, 2014-04-21 06:47
Normal topic Fragment files
by exchhattu » Fri, 2009-09-18 01:04 		4
 4,821 by rmoretti
Tue, 2015-01-06 09:58
Normal topic UBQ chemically conjugated docking error
by cheyuk » Fri, 2015-09-18 06:57 		4
 4,804 by cheyuk
Sun, 2015-09-20 02:08
Normal topic computer shuts down during autobulding with rosetta
by intekhab » Tue, 2011-07-19 01:07 		4
 4,460 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problems installing Rosetta
by S » Fri, 2010-09-03 01:04 		4
 6,247 by abdullah_ahmed
Mon, 2014-04-21 06:47
Normal topic Picking the correct model from a large set of decoys (30,000+)
by brspurri » Thu, 2012-04-26 15:37 		4
 5,775 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Relax protocol details for Rosetta 3.1
by Matthys » Sun, 2012-01-15 10:00 		4
 4,650 by rmoretti
Mon, 2014-04-21 06:47
Normal topic [Mover] is not known to the MoverFactory
by Jhreed » Fri, 2016-08-05 12:23 		4
 4,380 by msardejani
Sun, 2016-08-07 17:49
Normal topic Can I compare binding affinity of different ligands using Rosetta?
by zg148119@ohio.edu » Sun, 2020-12-06 11:30 		4
 3,531 by nannemdp
Fri, 2021-02-05 06:49
Normal topic pepspec aplication - segmentation fault
by tiagogomes89 » Fri, 2011-09-02 11:18 		4
 4,373 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ab initio/relax flag file setup
by w107kdk » Fri, 2009-08-28 11:49 		4
 4,837 by w107kdk
Mon, 2014-04-21 06:47
Normal topic RNA Parameter File
by hdavis9 » Tue, 2010-07-06 11:36 		4
 4,106 by smlewis
Mon, 2014-04-21 06:47
Normal topic rs filter for terms in .sc files
by gw » Sat, 2012-08-18 16:20 		4
 4,862 by gw
Mon, 2014-04-21 06:47
Normal topic problem parsing a THR residue
by decrSTL » Wed, 2019-08-21 12:25 		4
 3,111 by decrSTL
Tue, 2019-08-27 10:24
Normal topic multiple cst files
by logandonaldson » Wed, 2013-03-20 12:16 		4
 4,653 by logandonaldson
Mon, 2014-04-21 06:47
Normal topic Iterative local rebuilding vs automated structure refinement
by ahmadkhalifa » Fri, 2018-09-14 07:44 		4
 3,736 by rmoretti
Wed, 2018-11-21 14:11
Normal topic rosetta 3.1 recognizes PO4 group in dockinglocalrefine option?
by nilkoeg » Thu, 2011-03-10 23:19 		4
 5,574 by nilkoeg
Mon, 2014-04-21 06:47
Normal topic Random seed confusion
by pardave » Mon, 2012-11-12 09:45 		4
 4,865 by pardave
Mon, 2014-04-21 06:47
Normal topic RosettaCM rename or swap the order of sequences in your alignment file
by ahmadkhalifa » Fri, 2017-12-22 08:42 		4
 4,017 by rmoretti
Mon, 2018-01-15 15:24
Normal topic C-term amidation
by tttt » Tue, 2021-03-02 07:46 		4
 3,131 by tatsiana.bylund
Mon, 2022-01-24 07:58
Normal topic How can move peptide on cleft of enzyme on Flexpepdock?
by phanvy » Thu, 2014-06-05 02:22 		4
 4,724 by zaldini
Fri, 2015-01-02 05:38
Normal topic Problem with the -dock_ppk flag
by lzx32 » Sat, 2011-04-30 00:21 		4
 4,817 by lzx32
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 Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41 		4
 4,544 by linucks
Fri, 2018-02-23 08:08
Normal topic could I add some constrain to the backbone but not completely fix it when relax?
by albumns » Tue, 2010-06-29 05:43 		4
 4,049 by smlewis
Mon, 2014-04-21 06:47
Normal topic Ab initio structure prediction for long amino acid sequence
by maruhuang » Fri, 2019-08-02 03:38 		4
 3,237 by maruhuang
Thu, 2019-09-26 18:55
Normal topic Enzyme Design
by bharat_46010 » Tue, 2014-11-25 23:55 		4
 6,292 by bharat_46010
Mon, 2014-12-15 20:51
Normal topic The vall.jul19.2011.gz Database
by ac.research » Fri, 2017-09-01 02:29 		4
 4,719 by ac.research
Mon, 2017-09-04 16:43
Normal topic Does a negative Rosetta dG imply a favorable process?
by cossio » Tue, 2014-12-09 05:13 		4
 4,977 by lanselibai
Tue, 2014-12-16 10:48
Normal topic membrane protein packing prediction
by djpittdj » Fri, 2012-01-13 08:55 		4
 4,339 by pardave
Mon, 2014-04-21 06:47
Normal topic How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches
by zaldini » Fri, 2015-01-02 05:53 		4
 4,760 by zaldini
Wed, 2015-01-07 20:35
Normal topic error about 'std::bad_alloc' during running
by zhisheng » Mon, 2011-01-10 09:45 		4
 11,523 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to turn off output of POSE_ENERGIES_TABLE
by lah435 » Tue, 2015-02-03 21:21 		4
 4,636 by jwillis
Sat, 2015-02-07 20:40
Normal topic Comparative modeling Error: potential mismatch between sequence from alignment  and sequence from PDB!
by nzsuzsanna » Wed, 2016-04-27 05:32 		4
 5,014 by nzsuzsanna
Fri, 2016-04-29 04:30
Normal topic Antibody Homology Modeling - Antibody vs. Antibody_legacy
by cannond » Tue, 2017-02-14 05:53 		4
 4,331 by cannond
Wed, 2017-03-01 08:05
Normal topic Identical decoys
by aroop » Tue, 2012-09-25 12:50 		4
 4,821 by smlewis
Mon, 2014-04-21 06:47
Normal topic Seasons greetings with a Christmas tree shaped protein
by matteoferla » Sun, 2019-12-22 03:37 		4
 3,142 by matteoferla
Mon, 2019-12-23 07:24
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08 		4
 1,323 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic manually changing fixbb residue ref energies
by jtmacd » Wed, 2009-11-25 08:43 		4
 4,260 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Repeated entries in silent file
by almeida85 » Fri, 2022-08-05 02:52 		4
 1,599 by almeida85
Thu, 2022-08-11 00:29
Normal topic Successful installation on OpenSuse11.1 - tests?
by zharmad » Thu, 2010-08-19 00:30 		4
 3,997 by zharmad
Mon, 2014-04-21 06:47
Normal topic Fluctuations in I_sc
by eminegenetics » Thu, 2018-09-13 12:07 		4
 3,373 by eminegenetics
Fri, 2018-09-21 07:42
Normal topic short peptide fragment file generation
by cheyuk » Mon, 2016-07-11 00:04 		4
 4,842 by smlewis
Wed, 2016-07-13 23:41
Normal topic cluster error
by albumns » Thu, 2010-12-16 18:06 		4
 4,786 by smlewis
Mon, 2014-04-21 06:47
Normal topic Difference between score and silent_score when silent files are combined
by justin » Tue, 2012-01-03 06:44 		4
 4,545 by justin
Mon, 2014-04-21 06:47
Normal topic Error : seqpos <= size()
by phanvy » Sun, 2014-10-05 17:20 		4
 5,813 by phanvy
Wed, 2014-10-08 01:42
Normal topic Loop extensions at the end of chains
by japgar » Mon, 2010-07-26 12:35 		4
 4,362 by japgar
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 Error while running MakeRotLib
by saxen » Sun, 2016-04-17 22:51 		4
 4,806 by saxen
Mon, 2016-04-25 10:38
Normal topic rosetta 3.1-how to run parallel tasks?
by wtscrystal » Fri, 2009-11-06 03:23 		4
 6,098 by lqzhang
Mon, 2014-04-21 06:47
Normal topic rosettaScore.py has a typo, I think. Can I fix it in my own copy?
by mdeklotz » Thu, 2018-08-02 15:15 		4
 3,645 by rmoretti
Fri, 2018-08-03 11:39
Normal topic No values for total score while running Rosetta score file.
by Shweata Maurya » Wed, 2023-02-01 02:05 		4
 1,421 by Shweata Maurya
Wed, 2023-02-08 03:19
Normal topic [dev] Using h-bonding values in new energy term
by ipetrik_ambry » Wed, 2017-03-01 11:33 		4
 3,811 by ipetrik_ambry
Thu, 2017-03-02 15:35
Normal topic RosettaCM density guided rebuilding methodology
by ahmadkhalifa » Thu, 2018-08-30 06:45 		4
 3,450 by ahmadkhalifa
Thu, 2018-08-30 23:09
Normal topic Differentiable Energy Function w/ Centroid Representation
by protein_fan » Sun, 2022-03-20 09:39 		4
 1,759 by protein_fan
Fri, 2022-04-15 17:41
Normal topic enzdes error
by bo » Tue, 2012-08-21 09:12 		4
 4,434 by bo
Mon, 2014-04-21 06:47
Normal topic adding NCAA to the N-terminal of RCSB pdb
by ate » Tue, 2021-06-08 08:24 		4
 2,866 by Subhrodeep Saha
Sat, 2021-06-19 07:17
Normal topic an old question
by albumns » Sun, 2012-10-28 12:14 		4
 4,994 by rmoretti
Mon, 2014-04-21 06:47
Normal topic I generated a table of images & info of the premade NCAA params in the database
by matteoferla » Sun, 2020-02-16 06:27 		4
 3,127 by matteoferla
Sat, 2020-03-21 09:14
Normal topic using defined WATERS in PACKING
by ast » Wed, 2012-01-11 09:11 		4
 4,498 by smlewis
Mon, 2014-04-21 06:47
Normal topic Errors in scorefiles after running Design
by Jhreed » Tue, 2016-03-29 10:25 		4
 4,134 by smlewis
Wed, 2016-03-30 09:52
Normal topic Error using InterfaceHoles filter
by SenyorDrew » Fri, 2017-04-14 08:55 		4
 4,886 by SenyorDrew
Mon, 2017-07-24 11:06
Normal topic Updated publications/details on Rosetta score function?
by nitroamos » Tue, 2009-10-20 19:48 		4
 5,057 by rmoretti
Mon, 2015-03-30 14:43
Normal topic Introduction or tutorial about RosettaMatch
by kwak » Thu, 2010-10-21 06:37 		4
 6,581 by kwak
Mon, 2014-04-21 06:47
Normal topic params file for beta-amino acids
by phonez » Mon, 2021-03-29 18:30 		4
 2,803 by everyday847
Thu, 2021-04-01 11:59
Normal topic Errors in Interface design  
by Kazu » Thu, 2019-10-31 17:48 		4
 3,143 by Kazu
Mon, 2020-05-18 10:52
Normal topic unknown constraint function type: AtomPair ?
by jiongzhang » Sun, 2012-07-15 02:13 		4
 4,584 by jiongzhang
Mon, 2014-04-21 06:47
Normal topic What is virtual atom means in a params file and how to generate it？
by JasonIsaac » Fri, 2022-11-04 04:53 		4
 1,859 by JasonIsaac
Mon, 2022-11-07 19:15
Normal topic Question regarding Mlipo score
by DanielK » Tue, 2012-05-29 02:04 		4
 5,018 by smlewis
Mon, 2014-04-21 06:47
Normal topic Comparing scores
by renedominik » Mon, 2012-02-27 05:21 		4
 4,754 by renedominik
Mon, 2014-04-21 06:47
Normal topic What is the total_score that relax outputs?
by cossio » Tue, 2014-12-02 13:50 		4
 5,224 by cossio
Thu, 2014-12-04 05:41
Normal topic restrain multiple portions of proteins with MinMover
by Karol » Wed, 2016-09-07 08:29 		4
 5,018 by rmoretti
Thu, 2016-09-08 10:56
Normal topic DesignByCavityProximity: element not expected
by karenjgonzalez » Tue, 2020-01-28 05:16 		4
 2,924 by karenjgonzalez
Tue, 2020-02-11 08:44
Normal topic I have a .tab file. How do I extract information from it?
by monos_morpheus » Tue, 2011-02-08 09:30 		4
 5,458 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic postive score models from AbinitioRelax
by xpzhang » Fri, 2012-06-22 12:34 		4
 4,365 by smlewis
Mon, 2014-04-21 06:47
Normal topic Symmetric abrelax modeling
by SenyorDrew » Fri, 2011-02-18 10:14 		4
 4,592 by IAndre
Mon, 2014-04-21 06:47
Normal topic Membrane folding - blastpgp error.
by arthuc01 » Sun, 2012-03-25 14:47 		4
 5,948 by arthuc01
Mon, 2014-04-21 06:47
Normal topic Ligand conformations file in docking
by rosa » Fri, 2013-07-12 09:21 		4
 5,545 by rosa
Mon, 2014-04-21 06:48
Normal topic Denovo density corrupted silent file
by ahmadkhalifa » Mon, 2018-04-23 07:30 		4
 3,985 by ahmadkhalifa
Thu, 2018-04-26 09:11
Normal topic protein protein docking pipeline
by dzhao » Thu, 2012-07-19 06:25 		4
 6,059 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error when running enzyme_design tutorial
by linucks » Fri, 2017-06-30 12:26 		4
 3,941 by linucks
Mon, 2017-07-03 09:50
Normal topic Does Rosetta recognise OXT atom type in PDB.?
by monos_morpheus » Mon, 2011-04-11 23:57 		4
 5,596 by monos_morpheus
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 computer specifications
by rlwoltz » Tue, 2012-10-09 16:11 		4
 6,429 by rlwoltz
Mon, 2014-04-21 06:47
Normal topic how to keep native structure when do loop modeling
by zlni » Sun, 2009-05-03 10:12 		4
 4,409 by zlni
Mon, 2014-04-21 06:47
Normal topic a question about loop refinement
by albumns » Fri, 2012-03-02 09:38 		4
 5,700 by albumns
Mon, 2014-04-21 06:47
Normal topic Suppressing Rosetta output, flag for that?
by msellers » Tue, 2011-04-26 11:18 		4
 5,294 by smlewis
Mon, 2014-04-21 06:47
Normal topic How the Rosetta score (dG) is actually related to dH (enthalpy) and dS (entropy)?
by lanselibai » Thu, 2014-12-04 13:16 		4
 6,553 by lanselibai
Fri, 2014-12-12 10:27
Normal topic span and frags filefor multichain transmembrane protein
by zhiguang » Wed, 2016-10-26 13:28 		4
 4,200 by zhiguang
Tue, 2016-11-15 12:27
Normal topic RosettaMatch in 3.2
by jtmacd » Mon, 2010-12-20 08:04 		4
 5,167 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Discarding atoms for fixbb
by Jacob-kong » Tue, 2012-06-26 06:23 		4
 5,537 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic Give diferent chain information for a single sequence (comparative modeling)
by Martin Floor » Tue, 2013-04-02 08:59 		4
 4,881 by Martin Floor
Mon, 2014-04-21 06:47