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Rosetta 3 - General

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Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06
1
829 by lanselibai
Wed, 2021-06-23 14:53
Normal topic Structure refinement for helical assembles using Rosetta
by xiaoyanzi » Thu, 2020-06-18 00:34
0
828 by xiaoyanzi
Thu, 2020-06-18 00:36
Normal topic ligand docking error
by YuFei » Wed, 2020-04-22 17:27
0
824 by YuFei
Wed, 2020-04-22 17:27
Normal topic Searching density map using real space correlation
by ahmadkhalifa » Fri, 2018-12-28 00:28
0
822 by ahmadkhalifa
Fri, 2018-12-28 00:28
Normal topic Unrecognized atom parameter with denovo_density
by kalabharath » Mon, 2020-06-29 06:59
0
819 by kalabharath
Mon, 2020-06-29 06:59
Normal topic Rosetta and design of ligand binding site
by rohi » Mon, 2021-03-15 06:00
0
818 by rohi
Mon, 2021-03-15 06:31
Normal topic -ignore_unrecognized_res doesn't work
by e3lm » Fri, 2022-05-06 14:47
2
817 by e3lm
Fri, 2022-05-06 16:10
Normal topic Error: Element 'RandomizeBBByRamaPrePro': This element is not expected.
by nferruz » Fri, 2020-08-28 06:04
0
814 by nferruz
Fri, 2020-08-28 06:05
Normal topic Error with filter in rosseta_scripts
by Osmany Guirola » Mon, 2020-05-11 04:52
0
800 by Osmany Guirola
Mon, 2020-05-11 04:52
Normal topic The hbond for REF2015
by asbelx » Mon, 2022-06-06 06:07
2
798 by asbelx
Mon, 2022-06-06 23:15
Normal topic Comparatively modelled chains are far apart in final structure while the template pdb has all chains in a close-knit complex
by Sunidhi » Sun, 2020-11-01 11:00
0
795 by Sunidhi
Sun, 2020-11-01 11:01
Normal topic How RosettaCM can perform part of C terminal domain (CTD) structure prediction without proper template structures (coordinates)
by haom » Tue, 2020-09-01 13:21
0
794 by haom
Tue, 2020-09-01 18:50
Normal topic BUG REPORT: MySql column protocol.protocol_id must have the AUTO_INCREMENT flag set
by pedro.guillem » Wed, 2020-05-13 18:31
0
791 by pedro.guillem
Wed, 2020-06-24 04:42
Normal topic Does it make sense to perform Docking on a complex?
by chrisHKL » Mon, 2020-02-17 09:12
0
791 by chrisHKL
Mon, 2020-02-17 09:12
Normal topic I made a params file generation webpage
by matteoferla » Wed, 2020-07-22 03:08
0
787 by matteoferla
Wed, 2020-07-22 03:08
Normal topic Clustering error - Help, please
by karolcia1010 » Wed, 2020-06-17 11:19
0
778 by karolcia1010
Wed, 2020-06-17 11:19
Normal topic Using NCAA
by ate » Sat, 2021-05-01 02:22
0
777 by ate
Sat, 2021-05-01 02:22
Normal topic ab initio structure modeling
by pci112 » Mon, 2021-04-12 08:07
0
772 by pci112
Mon, 2021-04-12 08:12
Normal topic Docking mover
by Soler » Sat, 2022-02-12 20:48
1
767 by jadolfbr
Sat, 2022-02-12 23:16
Normal topic Finding affinity-reducing mutants towards a ligand in Ligand-based interface design protocol
by adityapadhi » Wed, 2020-06-24 01:29
0
767 by adityapadhi
Wed, 2020-06-24 01:29
Normal topic Compile C++ Rosetta to Pyrosetta ERROR
by michelleqyh » Fri, 2020-08-21 09:00
0
761 by michelleqyh
Fri, 2020-08-21 09:00
Normal topic Output "per-residue" energy score to database
by pedro.guillem » Thu, 2020-05-14 04:22
0
747 by pedro.guillem
Thu, 2020-05-14 04:22
Normal topic rna_denovo secstruct_general function
by rvandamme » Mon, 2021-02-01 13:39
0
742 by rvandamme
Mon, 2021-02-01 13:39
Normal topic connecting pdb files
by Hyun » Wed, 2021-11-17 22:32
1
738 by ajasja
Thu, 2021-11-18 00:33
Normal topic RNA update library
by Anne Klein » Mon, 2022-05-16 16:04
2
737 by Anne Klein
Tue, 2022-05-24 21:38
Normal topic Ensemble Docking with RosettaDock 4.0 Protocol
by mb0261 » Wed, 2022-07-27 07:00
1
735 by mb0261
Mon, 2022-09-26 07:50
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
0
730 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic Output and Input Tutorial
by jgustat » Fri, 2022-07-01 13:07
2
728 by jgustat
Fri, 2022-07-01 13:26
Normal topic Meaning of Metalbinding_constraint
by Corvin » Wed, 2021-05-19 07:54
0
725 by Corvin
Wed, 2021-05-19 07:54
Normal topic Make fragments
by jeanramos » Mon, 2020-07-13 00:56
0
720 by jeanramos
Mon, 2020-07-13 00:56
Normal topic Residue outside res_map range
by to-qinbin@163.com » Sat, 2022-09-10 01:56
1
718 by rmoretti
Mon, 2022-09-12 07:01
Normal topic score.sc only shows total_score and with all zeros
by johnnytam100 » Mon, 2022-06-06 20:04
2
700 by johnnytam100
Tue, 2022-06-07 19:18
Normal topic Quick mysql output question
by pedro.guillem » Thu, 2020-07-23 03:45
0
699 by pedro.guillem
Thu, 2020-07-23 03:45
Normal topic How to export high energy state pdb out of backrub?
by whiteqiu » Mon, 2021-03-01 18:32
0
695 by whiteqiu
Mon, 2021-03-01 18:32
Normal topic Inconsistent scoring by "aa_composition" term
by chenna » Thu, 2022-02-24 03:00
1
693 by vmulligan
Thu, 2022-03-03 18:48
Normal topic How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion
by wwwmrzkwww » Sun, 2021-08-15 00:19
0
691 by wwwmrzkwww
Sun, 2021-08-15 00:19
Normal topic De Novo backbone generation vs Rosetta Match for enzdes and ligand binding.
by csvajda » Thu, 2022-06-30 09:55
2
673 by csvajda
Thu, 2022-06-30 16:26
Normal topic undefined symbol: ZN9CifString12UnknownValueE error meaning?
by aniyaz » Wed, 2023-01-04 08:37
3
669 by aniyaz
Wed, 2023-01-11 01:24
Normal topic ERROR: Unable to open weights/patch file
by almeida85 » Tue, 2022-08-09 05:33
2
668 by almeida85
Thu, 2022-08-11 00:32
Normal topic Rosetta for design of artifical metalloenzyme
by Delfosse57 » Thu, 2022-05-19 21:47
1
664 by matteoferla
Fri, 2022-06-03 01:09
Normal topic Enzyme design gets 0 hit
by cryosky » Sun, 2021-09-26 13:24
0
663 by cryosky
Sun, 2021-09-26 13:24
Normal topic Renumbering PDB
by jgustat » Wed, 2022-07-27 13:37
2
658 by jgustat
Thu, 2022-07-28 10:00
Normal topic Save silent results to individual directory by process ID
by Payne » Sat, 2022-09-24 05:23
3
652 by rmoretti
Thu, 2022-09-29 00:15
Normal topic Segmentation fault on antibody structure prediction
by dkesar » Fri, 2021-06-04 19:09
0
651 by dkesar
Fri, 2021-06-04 19:09
Normal topic genkic mover produced an unwanted HN - CA bond
by cttm4a1 » Mon, 2022-06-20 14:25
2
650 by cttm4a1
Mon, 2022-06-20 16:58
Normal topic ERROR: Your compiler does not have full support for C++11 regex, and therefore can't support RegEx_based_CDR_Detector/antibody g
by yliang20 » Mon, 2022-08-08 16:59
1
642 by rmoretti
Tue, 2022-08-09 06:52
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32
2
638 by Ken
Wed, 2022-08-17 08:04
Normal topic enzyme design and scoring function
by rohi » Fri, 2021-06-25 10:29
0
626 by rohi
Fri, 2021-06-25 10:29
Normal topic Residue outside res_map range
by amcallister » Fri, 2022-04-22 11:26
1
617 by aneeqh
Fri, 2022-09-02 13:36
Normal topic Flex-pep-docking (ab-initio mode)
by ate » Wed, 2021-06-16 19:19
0
617 by ate
Wed, 2021-06-16 19:19
Normal topic SecundaryStructure Filter
by Soler » Sat, 2021-11-20 23:41
0
612 by Soler
Sat, 2021-11-20 23:41
Normal topic Obtain score during prediction
by CameronJA » Mon, 2021-06-14 16:12
0
609 by CameronJA
Mon, 2021-06-14 16:12
Normal topic InterfaceDdGMover and ResfileReader
by asaf.farhi » Wed, 2022-04-13 15:05
0
604 by asaf.farhi
Wed, 2022-04-13 15:05
Normal topic Obtaining all PDB IDs containing similar binding sites for a specific ligand
by Antonia » Wed, 2021-06-16 12:30
0
604 by Antonia
Wed, 2021-06-16 12:30
Normal topic Global ligand docking with Rosetta script and PyRosetta
by tisozaki » Tue, 2021-12-14 17:16
0
603 by tisozaki
Tue, 2021-12-14 17:16
Normal topic Where is Sicdock application now? Can I find a substitute?
by JasonIsaac » Sun, 2022-11-13 03:41
3
596 by rmoretti
Mon, 2022-11-14 07:27
Normal topic ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)
by Ken » Mon, 2022-05-23 07:16
1
590 by ajasja
Mon, 2022-05-23 07:19
Normal topic Applying dihedral constraints to TRP dipeptide minimization. ACE/NME termni.
by reoverstreet » Mon, 2022-07-11 14:39
1
588 by matteoferla
Wed, 2022-07-20 10:33
Normal topic RMSD filter
by Soler » Sat, 2022-01-15 22:09
0
583 by Soler
Sat, 2022-01-15 22:09
Normal topic No values for total score while running Rosetta score file.
by Shweata Maurya » Wed, 2023-02-01 02:05
4
579 by Shweata Maurya
Wed, 2023-02-08 03:19
Normal topic Problem with 'AddEncounterConstraintMover'
by mb0261 » Tue, 2022-06-28 10:00
1
565 by rmoretti
Tue, 2022-06-28 11:06
Normal topic mpi_MSD for antibody design
by hanzhiz » Thu, 2021-12-16 09:32
0
558 by hanzhiz
Thu, 2021-12-16 09:32
Normal topic Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting.
by ldx022 » Thu, 2023-03-09 17:03
3
553 by ldx022
Sat, 2023-03-11 16:53
Normal topic Error when using rna_denovo in TACC stampede2 HPC
by lsong2 » Thu, 2021-11-18 10:31
0
550 by lsong2
Thu, 2021-11-18 10:31
Normal topic Adding NCAA with Metal Ion
by MustafaBughio » Mon, 2022-11-28 15:07
1
549 by JasonIsaac
Mon, 2022-12-05 18:41
Normal topic Help with file in article Kemp elimination catalysts by computational enzyme design
by Wenithor » Sat, 2021-10-09 07:23
0
547 by Wenithor
Sat, 2021-10-09 07:23
Normal topic Generate template parameter file for a polymer
by anarob » Fri, 2022-06-10 11:05
1
546 by matteoferla
Fri, 2022-06-17 10:38
Normal topic Different dG_separated from RAbD and InterfaceAnalyzer
by brubin » Mon, 2022-12-19 13:58
2
537 by brubin
Tue, 2022-12-20 13:26
Normal topic SnugDock or RosettaDock for HDX-MS data
by hanzhiz » Thu, 2021-12-16 09:18
0
533 by hanzhiz
Thu, 2021-12-16 09:18
Normal topic ERROR: beta_nov16(.wts) requested, but -corrections::beta_nov16 not set to true. This leads to a garbage scorefunction.
by sia » Mon, 2023-05-08 06:36
6
524 by rmoretti
Tue, 2023-05-16 07:10
Normal topic mol2genparams.py script dependencies
by dhirajks » Wed, 2022-06-08 16:46
1
522 by matteoferla
Thu, 2022-06-09 14:41
Normal topic pose.energies().total_enegies().show_nonzero() changes after packer is applied
by Liviu Copoiu » Mon, 2022-11-07 16:51
2
518 by Liviu Copoiu
Tue, 2022-11-08 10:43
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08
4
510 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic Design strategy - One chain at a time OR two chains together?
by tlopes » Wed, 2022-01-05 18:19
0
505 by tlopes
Wed, 2022-01-05 18:19
Normal topic total_score changes when decomposing bb hbonds ref2015
by Liviu Copoiu » Mon, 2022-10-31 15:40
2
495 by Liviu Copoiu
Mon, 2022-10-31 16:03
Normal topic Error when attempting to relax pdb, "flag_input_relax" not found
by Wexter300 » Mon, 2023-01-23 11:32
4
494 by Wexter300
Wed, 2023-01-25 12:34
Normal topic Figuring out the input flags required for this script
by jjung380 » Wed, 2023-04-19 14:17
3
486 by rmoretti
Mon, 2023-05-15 15:23
Normal topic Score function in protein-protein docking with constrains
by Zehui Zhou » Mon, 2023-02-06 03:31
2
484 by Zehui Zhou
Wed, 2023-02-15 05:40
Normal topic Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi
by SamuelGong » Fri, 2023-01-27 06:20
3
483 by rmoretti
Mon, 2023-01-30 08:04
Normal topic protein binder interface design error
by guowuchen » Thu, 2022-06-23 04:43
0
480 by guowuchen
Thu, 2022-06-23 04:43
Normal topic Using specific rotamers
by sahn97 » Fri, 2022-08-26 13:45
1
475 by rmoretti
Fri, 2022-08-26 14:51
Normal topic PDB weird to PDB rosetta friendly
by jpfuenzalidawx » Fri, 2022-09-02 04:43
1
471 by rmoretti
Tue, 2022-09-06 08:13
Normal topic Multiple Relax runnings
by mb0261 » Sat, 2022-08-27 05:42
1
471 by rmoretti
Tue, 2022-09-06 08:22
Normal topic clean_pdb_keep_ligand.py IndexError
by to-qinbin@163.com » Sat, 2022-09-10 04:04
1
468 by rmoretti
Mon, 2022-09-12 06:58
Normal topic Unrecognized D-Leu name / C-terminal ACE
by almeida85 » Thu, 2022-08-11 07:43
1
456 by almeida85
Fri, 2022-08-12 05:56
Normal topic Sequence symmetry during FastDesign for repeat protein design
by cttm4a1 » Tue, 2022-09-06 21:02
1
451 by rmoretti
Wed, 2022-09-07 09:19
Normal topic Unexpected length of light chain FR1
by mgupta » Fri, 2022-12-09 01:03
0
431 by mgupta
Fri, 2022-12-09 01:03
Normal topic Run protein-protein docking parallelly by mpi
by Zehui Zhou » Thu, 2023-02-02 06:23
3
429 by Zehui Zhou
Fri, 2023-02-03 05:51
Normal topic rosetta scripts to superimpose multiple segments
by rlwoltz » Fri, 2022-04-29 15:15
0
422 by rlwoltz
Fri, 2022-04-29 15:15
Normal topic Intel MPI: early exit due to job process stopped.
by jackzzs » Mon, 2023-05-15 02:57
0
408 by jackzzs
Mon, 2023-05-15 03:17
Normal topic Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?
by JW_24 » Tue, 2023-01-24 04:40
2
406 by JW_24
Tue, 2023-01-24 14:52
Normal topic Question about remodelling
by tonycheng1688 » Mon, 2022-04-25 13:51
0
405 by tonycheng1688
Mon, 2022-04-25 13:51
Normal topic core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP
by to-qinbin@163.com » Wed, 2022-09-14 06:06
1
404 by rmoretti
Wed, 2022-09-14 09:14
Normal topic Ensemble file required for both partners with docking prepack protocol
by katherinemccoy » Tue, 2022-03-29 14:26
0
398 by katherinemccoy
Tue, 2022-03-29 14:26
Normal topic Calculating shape complementarity of ligand and protein
by varunmc99 » Tue, 2023-01-17 11:29
1
394 by rmoretti
Mon, 2023-02-06 14:42
Normal topic Predicting structure of protein after a few mutations
by Delfosse57 » Thu, 2022-12-01 20:40
0
390 by Delfosse57
Thu, 2022-12-01 20:40
Normal topic Prepacking crashing using metalloprotein
by mb0261 » Tue, 2022-12-06 10:16
0
385 by mb0261
Tue, 2022-12-06 10:16
Normal topic What should I do to lower down the fa_sol scores?
by JasonIsaac » Mon, 2022-12-05 18:57
0
385 by JasonIsaac
Mon, 2022-12-05 18:57
Normal topic RuntimeError: CUDA out of memory.
by ravi.thakkar » Tue, 2023-03-07 00:27
2
381 by rmoretti
Tue, 2023-03-07 08:18
Normal topic Loop modeling
by Robertofg » Tue, 2022-11-22 00:34
0
373 by Robertofg
Tue, 2022-11-22 00:34
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