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Rosetta 3 - General

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Normal topic How do I add virtual atom to my cofactor (metal ion) in rosettadock?
by monos_morpheus » Sat, 2011-02-05 21:24
2
2,633 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic Installing Rosetta Abinitio make_fragments.pl
by ctaylor » Thu, 2009-09-17 09:20
2
2,636 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Multiple jobs for homology modeling
by justin » Fri, 2011-06-24 08:03
1
2,642 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to set the cyana format of distance restraint in rosetta?
by zhisheng » Mon, 2011-04-25 02:21
1
2,643 by smlewis
Mon, 2014-04-21 06:47
Normal topic Library of unnatural amino acid parameters
by saxen » Mon, 2017-04-17 11:08
1
2,646 by smlewis
Tue, 2017-04-18 08:33
Normal topic Error score_scatter_plot.py
by jrcf » Wed, 2015-12-30 05:46
2
2,655 by jrcf
Fri, 2016-02-12 16:41
Normal topic Error when running enzyme_design tutorial
by linucks » Fri, 2017-06-30 12:26
4
2,662 by linucks
Mon, 2017-07-03 09:50
Normal topic What is "residue packing", "repacking", and so on?
by cossio » Wed, 2014-12-03 08:49
2
2,667 by cossio
Wed, 2014-12-03 14:51
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31
3
2,668 by rmoretti
Mon, 2014-04-21 06:48
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
2,668 by zhisheng
Mon, 2014-04-21 06:47
Normal topic Error when using RabD with a nanobody.
by zhangying1990 » Mon, 2018-12-17 04:40
5
2,673 by jadolfbr
Mon, 2019-01-28 08:46
Normal topic question about scoring silent output files and their contents
by burkheadlab » Wed, 2011-07-27 16:28
2
2,673 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to import SymmDock models into Rosetta for local docking and energy minimization
by devroop » Fri, 2012-07-20 13:20
1
2,678 by smlewis
Mon, 2014-04-21 06:47
Normal topic When does Rosetta switch from centroid to FA mode?
by MarkW » Fri, 2015-07-03 04:48
3
2,679 by rmoretti
Sun, 2015-07-05 14:28
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06
2
2,686 by vanita
Mon, 2014-04-21 06:47
Normal topic Question about run FLEXPEPDOCK with 3 chain
by phanvy » Wed, 2014-07-02 08:46
3
2,688 by phanvy
Wed, 2014-07-02 23:32
Normal topic obtaing pdb files
by knutjbj » Fri, 2011-02-25 11:05
3
2,689 by scombs
Mon, 2014-04-21 06:47
Normal topic How to insert a TER line between docking partners
by devroop » Sun, 2012-07-29 13:48
1
2,691 by smlewis
Mon, 2014-04-21 06:47
Normal topic Only 430 models are generated for membrane prediction
by justin » Wed, 2010-01-06 00:04
3
2,698 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problems with output control
by Sunyp_IM » Thu, 2017-06-22 15:30
3
2,708 by rmoretti
Wed, 2017-06-28 01:33
Normal topic about the option -constraints:cst_fa_file & -constraints:cst_fa_weight
by jiongzhang » Sat, 2010-12-25 12:55
1
2,715 by smlewis
Mon, 2014-04-21 06:47
Normal topic Clustering and Protein Preparation for docking
by MRH » Sun, 2013-08-25 22:01
1
2,716 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41
4
2,730 by linucks
Fri, 2018-02-23 08:08
Normal topic fixbb program
by Lindsay » Tue, 2012-05-08 13:56
3
2,730 by AndrewLeaver-Fay
Mon, 2014-04-21 06:47
Normal topic Question about homology modelling
by DmitriiN » Sun, 2016-08-21 13:44
3
2,741 by smlewis
Mon, 2016-08-22 10:28
Normal topic why docking results are different?
by albumns » Sat, 2010-12-18 23:53
3
2,742 by smlewis
Mon, 2014-04-21 06:47
Normal topic NOE constraints with Rosetta 3.1
by mpiuzzi » Wed, 2010-02-24 02:40
3
2,743 by mpiuzzi
Mon, 2014-04-21 06:47
Normal topic demos/public/ideal_proteins Segmentation fault
by coomteng@gmail.com » Wed, 2018-03-07 00:15
5
2,744 by rmoretti
Thu, 2018-03-08 07:46
Normal topic interpreting score values in silent output file after running abinitiorelax
by burkheadlab » Wed, 2011-03-09 15:42
3
2,747 by smlewis
Mon, 2014-04-21 06:47
Normal topic Is it CS-HM Rosetta restraint derivation i.e cm_scripts in Rosetta 3.3 bundles?
by nh_prt » Tue, 2013-03-26 12:22
3
2,750 by smlewis
Mon, 2014-04-21 06:47
Normal topic protocols.jd2.JobDistributor: [ ERROR ]
by johnnytam100 » Thu, 2019-04-11 09:30
5
2,750 by jadolfbr
Tue, 2019-04-16 09:15
Normal topic Rosetta3.5 src/core/pack/dunbrack/RotamerLibrary.cc permission problem
by ytao » Fri, 2013-06-28 12:13
2
2,752 by ytao
Mon, 2014-04-21 06:48
Normal topic a question about protein-ligand docking in generating 1SW2 conformers
by Ryhon Wang » Wed, 2014-05-28 22:27
2
2,755 by rmoretti
Tue, 2014-06-03 11:45
Normal topic Models which are not recorded (Abinitio protocol)
by allan.ferrari » Fri, 2015-08-28 13:39
3
2,756 by rmoretti
Thu, 2015-09-17 12:42
Normal topic Creating new residue type for pyridoxal phosphate bound to lysine (LLP) [Solved]
by franfdez » Sat, 2012-01-28 11:39
1
2,758 by franfdez
Mon, 2014-04-21 06:47
Normal topic ERROR: PDB reader is ignoring atom
by phanvy » Wed, 2014-04-16 17:59
2
2,764 by phanvy
Mon, 2014-04-21 03:58
Normal topic Structure prediction based on template -> Documentation comparative modeling of protein structures
by maxebert » Sun, 2011-03-20 01:15
1
2,767 by rmoretti
Mon, 2014-04-21 06:47
Normal topic covalent ligand docking in Rosetta
by rohi » Mon, 2021-06-07 06:39
12
2,772 by matteoferla
Wed, 2021-07-14 04:03
Normal topic combine silent.out file
by venkatazb » Fri, 2016-07-22 05:22
1
2,779 by smlewis
Fri, 2016-07-22 07:31
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50
2
2,790 by doranhen
Mon, 2014-04-21 06:47
Normal topic Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation
by jurkm » Mon, 2011-05-02 03:00
1
2,794 by smlewis
Mon, 2014-04-21 06:47
Normal topic Re: Basic python scripts for File Manipulation
by bharat_46010 » Mon, 2011-03-14 19:44
1
2,809 by smlewis
Mon, 2014-04-21 06:47
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37
2
2,813 by smlewis
Mon, 2014-04-21 06:47
Normal topic backrub score different from calculated score
by attesor » Wed, 2014-04-09 07:34
3
2,814 by rmoretti
Thu, 2014-04-10 07:38
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
2,815 by rmoretti
Wed, 2014-12-03 18:52
Normal topic Quesition about Relax Mode
by crysta11 » Wed, 2009-10-21 09:57
3
2,819 by smlewis
Mon, 2014-04-21 06:47
Normal topic Unknow atom_name: LYS 1HZ in enzdes after match
by petrikigor » Fri, 2012-10-19 09:35
1
2,820 by rmoretti
Mon, 2014-04-21 06:47
Normal topic ERROR: f.check_fold_tree
by sudhar » Mon, 2010-08-23 08:59
3
2,826 by smlewis
Mon, 2014-04-21 06:47
Normal topic The question about  protonation of Rosetta
by asbelx » Tue, 2017-12-19 05:44
3
2,828 by rmoretti
Mon, 2018-01-15 15:34
Normal topic Abinitio starts at the 27th amino acid
by JadAbbass » Thu, 2013-08-29 05:38
3
2,834 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic Parallel computing in RosettaDock3.1?
by xhluo » Fri, 2010-09-03 02:31
3
2,834 by smlewis
Mon, 2014-04-21 06:47
Normal topic change DOF of NH3 group in N terminus
by SergeyP » Wed, 2016-02-03 02:22
3
2,837 by SergeyP
Thu, 2016-02-04 00:07
Normal topic DomainAssembly Mover with constraints (using RosettaScripts)
by resiros » Wed, 2016-09-21 11:19
3
2,837 by rmoretti
Mon, 2016-11-14 14:21
Normal topic Homology Model gives output - but completely wrong!
by Julix » Wed, 2012-10-31 10:10
1
2,839 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaDesign Server, reproducing optimized interface conformation
by AlexanderMetz » Thu, 2012-02-09 10:41
1
2,842 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error when clustering the output from a docking study
by jos » Thu, 2011-09-08 03:26
2
2,847 by jos
Mon, 2014-04-21 06:47
Normal topic error when running beta_strand_homodimer_design
by szypanther » Sun, 2014-05-25 20:22
2
2,865 by szypanther
Mon, 2014-05-26 22:03
Normal topic Docking 2 proteins including ligands
by einew » Tue, 2011-03-08 13:33
3
2,871 by einew
Mon, 2014-04-21 06:47
Normal topic Negative design: Can a filter call a mover in rosetta scripts?
by jgans » Sat, 2012-09-08 21:28
2
2,874 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to generate constraints of active sites from a pdb file of an enzyme
by Albert » Sun, 2013-05-26 20:07
3
2,875 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic positive results in total_score by symmetry docking
by Jacob » Thu, 2011-06-16 05:18
1
2,881 by rmoretti
Mon, 2014-04-21 06:47
Normal topic first run of abinitio in rosetta 3.2 produces an error right away
by burkheadlab » Fri, 2011-03-04 22:50
3
2,891 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaHoles?
by kbala » Thu, 2009-07-30 16:52
3
2,904 by smlewis
Mon, 2014-04-21 06:47
Normal topic Efficient implementation of MPI with protein design programs
by zachdebruine » Thu, 2018-06-28 10:41
5
2,911 by smlewis
Tue, 2018-07-03 11:22
Normal topic dna_denovo
by frits » Fri, 2013-07-12 06:12
3
2,913 by frits
Mon, 2014-04-21 06:48
Normal topic Error running design in 3.4
by inder » Thu, 2012-07-05 19:27
2
2,913 by inder
Mon, 2014-04-21 06:47
Normal topic what option should I use if I want to use the dfire in 3.4
by Lindsay » Thu, 2012-04-12 05:19
3
2,917 by smlewis
Mon, 2014-04-21 06:47
Normal topic span and frags filefor multichain transmembrane protein
by zhiguang » Wed, 2016-10-26 13:28
4
2,919 by zhiguang
Tue, 2016-11-15 12:27
Normal topic calculate low-resolution total docking score for a input pdb
by jasnyderjr » Fri, 2015-12-11 23:08
3
2,920 by rmoretti
Wed, 2015-12-16 11:22
Normal topic Comparison between two fragment pickers
by qlj » Mon, 2013-09-02 06:34
3
2,922 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Pairwise decomposable terms in the Rosetta energy function
by pgainza » Wed, 2011-08-03 12:26
1
2,929 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Errors in scorefiles after running Design
by Jhreed » Tue, 2016-03-29 10:25
4
2,929 by smlewis
Wed, 2016-03-30 09:52
Normal topic Successful installation on OpenSuse11.1 - tests?
by zharmad » Thu, 2010-08-19 00:30
4
2,931 by zharmad
Mon, 2014-04-21 06:47
Normal topic Cluster gdtmm vs. rmsd
by brspurri » Thu, 2012-04-19 08:20
1
2,933 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Solving van der waals clashes in a transmembrane protein model with rosetta
by doranhen » Wed, 2012-12-05 00:12
3
2,933 by smlewis
Mon, 2014-04-21 06:47
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
2,935 by rmoretti
Mon, 2014-04-21 06:48
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
2,936 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop Modelling: ERROR: switch_to_residue_type_set fails
by smiruthi » Wed, 2012-07-18 14:48
2
2,937 by smlewis
Mon, 2014-04-21 06:47
Normal topic Troubles using RigidBodyTransMover and RigidBodyPerturbMover
by alejandro » Thu, 2011-04-21 06:11
3
2,938 by alejandro
Mon, 2014-04-21 06:47
Normal topic Rosetta can't handle symmetric fold and dock for >10-subunit protein?
by myang » Mon, 2011-09-26 11:52
3
2,939 by IAndre
Mon, 2014-04-21 06:47
Normal topic Make_fragments.pl database
by TiagoGomes » Tue, 2009-10-13 11:31
5
2,942 by matteoferla
Wed, 2021-09-29 01:58
Normal topic how to keep modeling ignored ERROR?
by eunwook » Sat, 2013-04-27 05:44
3
2,949 by eunwook
Mon, 2014-04-21 06:47
Normal topic Calling a Rosetta xml script in a Python script gives fail to validate error
by ahmadkhalifa » Tue, 2018-03-06 08:00
3
2,955 by rmoretti
Mon, 2018-03-19 12:35
Normal topic Fix missing backbone residues
by Matthys » Mon, 2010-05-03 09:03
2
2,956 by Matthys
Mon, 2014-04-21 06:47
Normal topic Adding new files using rosetta classes went wrong
by Jeremy1990 » Sun, 2015-04-26 01:07
3
2,959 by rmoretti
Thu, 2015-04-30 16:09
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
2,960 by smlewis
Wed, 2017-11-08 12:08
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59
2
2,961 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Rosetta numbering with missing occupancies
by ShaneOConnor » Fri, 2011-10-07 16:18
2
2,962 by ShaneOConnor
Mon, 2014-04-21 06:47
Normal topic The following options have been set but have not yet been used
by jrcf » Fri, 2015-10-09 10:48
2
2,963 by jrcf
Fri, 2015-10-16 10:57
Normal topic Problems with disulphide bonds during KIC
by Loki01 » Tue, 2017-11-28 03:11
5
2,965 by Loki01
Thu, 2017-12-14 06:20
Normal topic Simple FoldTree Question
by gipsonb » Wed, 2012-04-25 18:19
3
2,988 by gipsonb
Mon, 2014-04-21 06:47
Normal topic AtomPair and SPLINE
by attesor » Sat, 2015-06-20 11:42
2
2,994 by attesor
Thu, 2015-10-22 03:42
Normal topic -loops:refine_repack_cycles option not accepted by loopmodel.linuxgccrelease
by tsjain » Tue, 2013-02-05 18:47
3
3,005 by tsjain
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,008 by smlewis
Mon, 2014-04-21 06:47
Normal topic make_fragments
by sumukh21 » Wed, 2011-02-23 09:29
3
3,009 by sumukh21
Mon, 2014-04-21 06:47
Normal topic RNA Parameter File
by hdavis9 » Tue, 2010-07-06 11:36
4
3,010 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
3,011 by Jeffrey_Chen
Tue, 2014-03-25 23:06
Normal topic Secondary Structure Relax
by ac.research » Sat, 2018-03-17 10:50
5
3,017 by smlewis
Wed, 2018-03-21 08:42
Normal topic Modeling protonated histidine
by SenyorDrew » Mon, 2016-07-18 07:34
3
3,019 by matteoferla
Sat, 2017-08-05 07:18
Normal topic Error when running "plot_LHOC.py"
by Sunyp_IM » Sun, 2017-08-13 05:54
5
3,022 by smlewis
Wed, 2017-08-16 08:30
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