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Rosetta 3 - Applications
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Topic / Topic starter | Replies | Views | Last post | |
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clustering output file has few structures by fabiotrovato » Mon, 2020-08-17 11:37 |
0 |
767 |
by fabiotrovato Mon, 2020-08-17 11:37 |
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RosettaCM by jlawrie » Fri, 2020-08-14 14:09 |
0 |
1,499 |
by jlawrie Fri, 2020-08-14 14:09 |
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mpirun docking_protocol by NanB » Mon, 2020-08-03 11:38 |
1 |
2,868 |
by ssrb Fri, 2020-08-14 09:18 |
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Docking-I_sc values do not correlate by jlawrie » Wed, 2020-08-12 08:08 |
2 |
1,751 |
by jlawrie Wed, 2020-08-12 08:57 |
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Homology Modeling-no PDB output by jlawrie » Wed, 2020-08-12 06:30 |
2 |
1,840 |
by jlawrie Wed, 2020-08-12 08:56 |
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Modeling-Using RosettaCM by jlawrie » Wed, 2020-08-12 08:46 |
1 |
1,101 |
by jlawrie Wed, 2020-08-12 08:47 |
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Docking-RMS value nan by jlawrie » Wed, 2020-08-12 07:03 |
2 |
1,817 |
by jlawrie Wed, 2020-08-12 07:27 |
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Error when trying docking protocol with different ligand by scyphs » Wed, 2020-08-05 04:37 |
2 |
1,573 |
by scyphs Mon, 2020-08-10 08:09 |
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how to know the precedure of solving a actural bio problem? like interface design? by qq7678500549 » Thu, 2020-08-06 18:45 |
2 |
1,554 |
by qq7678500549 Sun, 2020-08-09 18:59 |
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De novo water predictions using SPaDES by MNP1986 » Mon, 2019-03-25 07:53 |
1 |
1,795 |
by matteoferla Tue, 2020-08-04 09:30 |
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Bug Report - Encoding issue by daniloboskovic » Tue, 2020-08-04 07:02 |
0 |
749 |
by daniloboskovic Tue, 2020-08-04 07:02 |
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pepspec anchor dock by Andre Serobian » Tue, 2020-07-28 05:51 |
1 |
1,219 |
by Andre Serobian Tue, 2020-07-28 23:26 |
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Zero residues error in docking by cjy318 » Tue, 2020-07-28 19:47 |
0 |
1,084 |
by cjy318 Tue, 2020-07-28 19:47 |
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RosettaAntibody3 core.pose.util error by linhhoang157 » Tue, 2020-07-28 12:40 |
0 |
992 |
by linhhoang157 Tue, 2020-07-28 12:40 |
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clean_pdb not working by Andre Serobian » Thu, 2020-07-23 04:48 |
3 |
2,513 |
by rmoretti Tue, 2020-07-28 08:24 |
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Comparative modeling of metalloproteins by ctqwong » Sun, 2020-07-12 13:51 |
3 |
2,075 |
by ctqwong Mon, 2020-07-27 01:48 |
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How many iterations of remodel is enough? by daniloboskovic » Thu, 2020-07-16 08:07 |
0 |
825 |
by daniloboskovic Thu, 2020-07-16 08:14 |
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Translate mover chain X doesnot exist. by surya » Thu, 2020-07-09 08:36 |
6 |
3,345 |
by rmoretti Tue, 2020-07-14 10:54 |
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Warning: Fold tree is not set properly for density scoring by ahansel » Mon, 2020-07-13 10:50 |
1 |
1,341 |
by danpf Tue, 2020-07-14 10:27 |
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Problem with mpirun/mpiexec by ahansel » Fri, 2020-07-10 08:37 |
1 |
3,702 |
by rmoretti Fri, 2020-07-10 09:59 |
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Segmentation Fault during prepacking by Sunyp_IM » Fri, 2020-06-12 11:24 |
4 |
3,237 |
by Sunyp_IM Thu, 2020-07-09 18:40 |
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Metal Ion in symmetric design by tschiex » Wed, 2020-07-08 05:28 |
0 |
866 |
by tschiex Wed, 2020-07-08 05:28 |
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PEPSPEC by Neeraj » Wed, 2018-01-03 02:24 |
1 |
1,802 |
by Andre Serobian Wed, 2020-07-08 04:44 |
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Does antibody_numbering_converter support camelid antibody? by mxp » Tue, 2020-07-07 01:21 |
0 |
882 |
by mxp Tue, 2020-07-07 01:21 |
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zero standard deviation of I_sc in protein-protein docking by rohi » Fri, 2020-07-03 22:19 |
0 |
822 |
by rohi Fri, 2020-07-03 22:20 |
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OptimizeMembranePositionMover - This element is not expected by bjharris » Wed, 2020-07-01 23:21 |
2 |
1,911 |
by bjharris Thu, 2020-07-02 11:09 |
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LoopModeler mover unable to determine cut point by gszwabowski » Mon, 2020-06-01 13:12 |
1 |
1,577 |
by matteoferla Thu, 2020-07-02 07:27 |
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ligand_docking: ligand preparation by Alison_Yajie » Thu, 2020-07-02 07:05 |
0 |
896 |
by Alison_Yajie Thu, 2020-07-02 07:10 |
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kcenters_clustering_of_fragments by bjharris » Mon, 2019-07-01 16:16 |
1 |
1,514 |
by bjharris Wed, 2020-07-01 23:25 |
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Scoring after HBNet by HHL_SIUC » Wed, 2020-07-01 10:49 |
0 |
853 |
by HHL_SIUC Wed, 2020-07-01 10:49 |
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"core.kinematics.FoldTree" error upon running RAbD by Sunyp_IM » Fri, 2020-06-26 17:27 |
2 |
1,778 |
by Sunyp_IM Fri, 2020-06-26 20:57 |
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ligand_docking ligand preparation by Alison_Yajie » Thu, 2020-05-21 10:21 |
2 |
1,627 |
by Alison_Yajie Wed, 2020-06-24 12:38 |
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Ligand docking with constraint by Alison_Yajie » Wed, 2020-06-24 12:34 |
0 |
851 |
by Alison_Yajie Wed, 2020-06-24 12:34 |
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How to create a native file for Protein-Protein docking by Kotimedidhi » Fri, 2020-06-19 08:58 |
2 |
1,731 |
by Kotimedidhi Mon, 2020-06-22 16:19 |
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How to select docked models by Sunyp_IM » Mon, 2020-06-22 00:50 |
1 |
1,196 |
by ssrb Mon, 2020-06-22 13:12 |
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Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex by benhardy » Mon, 2020-06-15 09:33 |
3 |
2,160 |
by benhardy Fri, 2020-06-19 07:55 |
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Residue selector by Alison_Yajie » Wed, 2020-06-17 19:57 |
0 |
861 |
by Alison_Yajie Thu, 2020-06-18 09:47 |
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Constraint generator by Alison_Yajie » Wed, 2020-06-17 20:14 |
1 |
1,179 |
by Alison_Yajie Wed, 2020-06-17 20:35 |
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metalloprotein ab initio with glutamic acid by inorgchem » Tue, 2020-06-16 20:45 |
0 |
718 |
by inorgchem Tue, 2020-06-16 20:45 |
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RosettaCM: An internal error has occurred when "Running the Hybridize mover" by haom » Mon, 2020-06-15 05:56 |
4 |
2,437 |
by haom Tue, 2020-06-16 05:55 |
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The difference between the H1 regions of modeled camelid antibody and the crystal structure. by Sunyp_IM » Sun, 2020-06-07 02:34 |
1 |
1,335 |
by nannemdp Sun, 2020-06-07 08:01 |
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The usage of antibody_H3.linuxgccrelease by Sunyp_IM » Thu, 2020-05-28 22:50 |
2 |
1,966 |
by Sunyp_IM Thu, 2020-06-04 08:20 |
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"Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease by Sunyp_IM » Thu, 2020-06-04 05:53 |
0 |
877 |
by Sunyp_IM Thu, 2020-06-04 05:54 |
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RosettaAntibodyDesign: How can I run the protocol without allowing design? by brspurri » Tue, 2020-05-26 08:12 |
5 |
2,932 |
by brspurri Wed, 2020-06-03 13:20 |
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AbinitioRelax detect_disulf_tolerance by aarono » Tue, 2020-06-02 00:13 |
0 |
912 |
by aarono Tue, 2020-06-02 00:13 |
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ligand_docking_error by Alison_Yajie » Mon, 2020-04-20 12:27 |
3 |
2,248 |
by YuFei Sat, 2020-05-30 00:12 |
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Problems with mpi version of antibody.linuxgccrelease by Sunyp_IM » Thu, 2020-05-28 23:06 |
0 |
1,078 |
by Sunyp_IM Thu, 2020-05-28 23:07 |
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mp_transform optimize with franklin2019 scoring by benhardy » Thu, 2020-05-28 08:35 |
0 |
1,230 |
by benhardy Thu, 2020-05-28 08:45 |
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What is a rational minimal value for the "-nstruct" option by Sunyp_IM » Fri, 2020-05-22 01:28 |
3 |
2,159 |
by nannemdp Sun, 2020-05-24 14:46 |
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cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues by ValentinaSora » Sun, 2020-05-24 12:32 |
0 |
1,405 |
by ValentinaSora Sun, 2020-05-24 12:32 |
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relax and movemap by Alison_Yajie » Wed, 2020-05-20 21:27 |
3 |
2,269 |
by smlewis Thu, 2020-05-21 21:05 |
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Changing rosetta scoring to favour less hydrophobic areas by daniloboskovic » Thu, 2020-05-21 03:03 |
1 |
1,222 |
by vmulligan Thu, 2020-05-21 18:33 |
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ligand_docking: ligand preparation by Alison_Yajie » Thu, 2020-05-21 09:42 |
0 |
950 |
by Alison_Yajie Thu, 2020-05-21 09:42 |
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Modelling temperature dependent RNA structures by tuleshwori » Tue, 2020-05-19 01:16 |
2 |
1,700 |
by tuleshwori Thu, 2020-05-21 02:08 |
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Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1 by cm21 » Wed, 2020-05-20 08:55 |
2 |
1,789 |
by cm21 Wed, 2020-05-20 11:22 |
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Rna Denovo by helderveras » Wed, 2020-05-06 08:40 |
5 |
3,037 |
by everyday847 Wed, 2020-05-20 08:52 |
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Side-chain grafting at the fixed protein and position by Kazu » Wed, 2020-05-20 08:49 |
0 |
807 |
by Kazu Wed, 2020-05-20 08:49 |
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Transmembrane helix fold-and-dock? by sarah_b » Tue, 2020-05-12 02:09 |
3 |
2,302 |
by jkleman Tue, 2020-05-19 15:02 |
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protein relax by Alison_Yajie » Tue, 2020-05-19 08:29 |
0 |
890 |
by Alison_Yajie Tue, 2020-05-19 08:29 |
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RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow? by brspurri » Thu, 2020-05-14 11:15 |
2 |
1,648 |
by brspurri Thu, 2020-05-14 12:24 |
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Flex_ddG crashes when attempting to move 2 chains (e.g. chains_to_move = A,C) by jcampecino » Wed, 2020-05-13 12:22 |
0 |
1,067 |
by jcampecino Wed, 2020-05-13 12:22 |
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How to run partial_thread in RosettaCM when residure are more than 9999? by lanselibai » Mon, 2020-05-11 22:43 |
2 |
2,181 |
by lanselibai Tue, 2020-05-12 20:25 |
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How to concatenate the 3-mer and 9-mer files for RosettaCM? by lanselibai » Fri, 2020-05-08 05:38 |
5 |
3,275 |
by danpf Tue, 2020-05-12 10:58 |
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Template/Input length mismatch error during RosettaCM by marinok » Mon, 2020-05-04 13:12 |
4 |
2,714 |
by marinok Mon, 2020-05-11 12:48 |
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General question regarding ligand-docking by Alison_Yajie » Thu, 2020-05-07 09:48 |
0 |
799 |
by Alison_Yajie Thu, 2020-05-07 09:48 |
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Can the Rosetta Antibody Design (RAbD) protocol incorporate glycans? by ccottrell » Tue, 2020-05-05 20:30 |
5 |
2,950 |
by jadolfbr Wed, 2020-05-06 11:37 |
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Ligand docking at specific orientation by ShiranBZ » Mon, 2020-04-13 20:46 |
1 |
1,225 |
by matteoferla Mon, 2020-05-04 02:02 |
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can remodel add loops in one chain in multichain PDB structure? by ksteczk » Fri, 2020-05-01 06:26 |
1 |
1,444 |
by matteoferla Mon, 2020-05-04 01:43 |
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BUG REPORT: Remodel Resfile ERROR: LEU was added more than once? by daniloboskovic » Wed, 2020-04-29 01:17 |
2 |
1,784 |
by daniloboskovic Wed, 2020-04-29 05:51 |
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RosettaDesign error with Option file open failed by xingqing326 » Sun, 2020-04-19 01:56 |
4 |
3,929 |
by xingqing326 Tue, 2020-04-21 19:11 |
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DNA-protein docking by ksteczk » Sat, 2020-04-11 11:23 |
0 |
1,374 |
by ksteczk Sat, 2020-04-11 11:23 |
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Use membrane or non-membrane weights in RosettaCM for a hexon in virus capsid? by lanselibai » Sat, 2020-04-11 02:10 |
0 |
966 |
by lanselibai Sat, 2020-04-11 02:10 |
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Rosetta remodel - including an RNA ligand by daniloboskovic » Fri, 2020-04-10 04:24 |
0 |
977 |
by daniloboskovic Fri, 2020-04-10 04:24 |
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Error with the mpi version of simple_cycpep_predict by Florent Langenfeld » Wed, 2020-02-05 05:16 |
5 |
3,192 |
by vmulligan Fri, 2020-04-10 02:54 |
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What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001." by Corvin » Thu, 2020-04-02 00:16 |
0 |
979 |
by Corvin Thu, 2020-04-02 00:16 |
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Docking of multichain oligomers by sdh_h » Wed, 2020-03-25 12:43 |
0 |
1,075 |
by sdh_h Wed, 2020-03-25 12:43 |
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Any progress on getting intermediate structures during a design? by broomsday » Mon, 2020-03-16 06:46 |
2 |
1,881 |
by vmulligan Tue, 2020-03-17 11:35 |
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application for affinity optimization by wentlewi » Fri, 2020-03-13 03:24 |
0 |
982 |
by wentlewi Fri, 2020-03-13 03:24 |
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Is native.pdb necess for fragment_picker? by ylwang » Thu, 2020-03-12 00:57 |
2 |
1,884 |
by ylwang Thu, 2020-03-12 20:42 |
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"sparks failed" error when running "make_fragments.pl"? by Danielsebas » Tue, 2019-09-03 03:43 |
6 |
4,091 |
by Jacob_Verburgt Tue, 2020-03-10 14:39 |
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score is 0 in the output? - RosettaScripts by chrisHKL » Thu, 2020-03-05 09:33 |
0 |
956 |
by chrisHKL Thu, 2020-03-05 12:58 |
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RosettaScript Segmentation Fault (crash log attached) by chrisHKL » Thu, 2020-03-05 07:21 |
2 |
2,396 |
by chrisHKL Thu, 2020-03-05 09:11 |
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std::bad_alloc error after changing .xml script? by chrisHKL » Wed, 2020-03-04 11:44 |
10 |
5,549 |
by jadolfbr Thu, 2020-03-05 07:02 |
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nstruct vs. trials? by chrisHKL » Mon, 2020-03-02 13:22 |
2 |
1,715 |
by chrisHKL Wed, 2020-03-04 10:49 |
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Comparative Modeling Templates for Protein with Multiple Domains by Morrian_Lynn » Wed, 2020-03-04 10:42 |
0 |
881 |
by Morrian_Lynn Wed, 2020-03-04 10:42 |
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Ddg filter threshold value? by chrisHKL » Fri, 2020-02-28 15:01 |
1 |
1,279 |
by rmoretti Wed, 2020-03-04 09:56 |
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Imitating induced fit protocol in SymDock2 without any symmetry constraints by chenna » Fri, 2020-02-14 01:35 |
2 |
1,941 |
by chenna Wed, 2020-03-04 03:24 |
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Filter for fixed-bb design using RosettaScript? by chrisHKL » Fri, 2020-02-28 19:47 |
4 |
2,513 |
by vmulligan Mon, 2020-03-02 13:40 |
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antibody_numbering_converter cannot recognize the IMGT scheme by cryosky » Sat, 2020-02-29 23:12 |
4 |
2,969 |
by jadolfbr Sun, 2020-03-01 14:54 |
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What is interface_cutoff_distance? And why did my residues outside this value get designed? by chrisHKL » Fri, 2020-02-28 14:52 |
0 |
1,014 |
by chrisHKL Fri, 2020-02-28 14:52 |
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remodel ERROR: unrecognized mm_atom_type_name RGU by daniloboskovic » Sat, 2020-02-22 11:55 |
1 |
1,479 |
by daniloboskovic Tue, 2020-02-25 08:28 |
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Rosetta scripts crash in CM workflow by jlburkhead » Tue, 2019-12-03 22:55 |
1 |
1,608 |
by danpf Fri, 2020-02-21 18:37 |
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Options "-out:prefix" didn't work by maruhuang » Tue, 2019-09-10 05:42 |
4 |
2,830 |
by danpf Fri, 2020-02-21 18:32 |
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Protein-Protein Docking or Comparative Modeling by Morrian_Lynn » Wed, 2020-01-29 19:01 |
1 |
1,363 |
by danpf Fri, 2020-02-21 18:23 |
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How can I model ligands in comparative modeling by Morrian_Lynn » Thu, 2020-02-20 09:57 |
1 |
1,263 |
by danpf Fri, 2020-02-21 17:05 |
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get an increased energy after energy minimization when using different score functions for repacking and energy minimization by xinmiaohe » Fri, 2020-02-07 11:59 |
1 |
1,391 |
by xinmiaohe Fri, 2020-02-07 13:52 |
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error: Unable to open weights/patch file in using ddg_monomer.linuxgccrelease by xinmiaohe » Thu, 2020-01-30 22:09 |
1 |
1,999 |
by xinmiaohe Fri, 2020-01-31 08:23 |
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Error during single state design by sujigeorge1979 » Sat, 2020-01-18 00:37 |
5 |
5,151 |
by rmoretti Thu, 2020-01-30 15:42 |
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fixing sequence during grafting in antibody_designer by COM » Fri, 2020-01-24 11:38 |
1 |
1,399 |
by jadolfbr Tue, 2020-01-28 09:13 |
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appropriate sampling for protein docking to a multi chain assembly by SWM » Fri, 2020-01-24 11:22 |
0 |
837 |
by SWM Fri, 2020-01-24 11:22 |
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