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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
7,471 by admin
Fri, 2015-09-04 16:17
Normal topic Error with xml script
by almeida85 » Tue, 2023-03-28 01:53
0
14 by almeida85
Tue, 2023-03-28 01:53
Normal topic Method for adding residues into PDB's w/ RosettaScripts.
by Wexter300 » Wed, 2023-03-15 13:07
1
108 by rmoretti
Thu, 2023-03-16 11:46
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
170 by ldx022
Sat, 2023-03-11 16:53
Normal topic RuntimeError: CUDA out of memory.
by ravi.thakkar » Tue, 2023-03-07 00:27
2
127 by rmoretti
Tue, 2023-03-07 08:18
Normal topic Error when trying to use xml script to design PDB
by Wexter300 » Fri, 2023-02-24 13:29
1
144 by rmoretti
Fri, 2023-02-24 13:58
Normal topic Which application/mover should I use to evaluate the ddg between apo enzyme and enzyme binding with transition state?
by JasonIsaac » Wed, 2023-02-22 18:36
0
133 by JasonIsaac
Wed, 2023-02-22 18:36
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
368 by rmoretti
Mon, 2023-02-20 16:07
Normal topic can't access rosetta commercial license download via given URL from CoMotion
by y_atsmonraz » Tue, 2023-02-14 11:04
8
237 by rmoretti
Thu, 2023-02-16 13:48
Normal topic Rosetta remodelling - how to change the added residue type instead of just VAL
by xuezhi » Wed, 2023-02-15 14:00
0
91 by xuezhi
Wed, 2023-02-15 14:00
Normal topic How to set jump between ligands
by Zehui Zhou » Wed, 2023-02-15 04:48
0
101 by Zehui Zhou
Wed, 2023-02-15 07:12
Normal topic Score function in protein-protein docking with constrains
by Zehui Zhou » Mon, 2023-02-06 03:31
2
161 by Zehui Zhou
Wed, 2023-02-15 05:40
Normal topic Truncating a protein using rosetta
by Wexter300 » Mon, 2023-02-13 12:05
2
109 by Wexter300
Mon, 2023-02-13 13:04
Normal topic Segmentation fault with nstruct > 1
by Brian Wiley » Sun, 2023-02-12 20:46
0
86 by Brian Wiley
Sun, 2023-02-12 20:46
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08
4
159 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic No values for total score while running Rosetta score file.
by Shweata Maurya » Wed, 2023-02-01 02:05
4
222 by Shweata Maurya
Wed, 2023-02-08 03:19
Normal topic Calculating shape complementarity of ligand and protein
by varunmc99 » Tue, 2023-01-17 11:29
1
207 by rmoretti
Mon, 2023-02-06 14:42
Normal topic Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.
by SubhaK » Thu, 2023-01-26 21:29
1
129 by rmoretti
Mon, 2023-02-06 14:35
Normal topic Error in H3_modeling_scores.fasc file from antibody_H3 program
by Brian Wiley » Sat, 2023-02-04 23:41
0
80 by Brian Wiley
Sat, 2023-02-04 23:43
Normal topic LHOC script problem in Rosetta Antibody
by ziheng@mit.edu » Thu, 2019-04-25 14:19
3
1,425 by Brian Wiley
Sat, 2023-02-04 23:26
Normal topic Run protein-protein docking parallelly by mpi
by Zehui Zhou » Thu, 2023-02-02 06:23
3
141 by Zehui Zhou
Fri, 2023-02-03 05:51
Normal topic Should all input structures to energy_based_clustering have an output pdb file?
by Brian Wiley » Mon, 2023-01-30 20:42
2
117 by Brian Wiley
Tue, 2023-01-31 19:08
Normal topic Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi
by SamuelGong » Fri, 2023-01-27 06:20
3
159 by rmoretti
Mon, 2023-01-30 08:04
Normal topic Error when attempting to relax pdb, "flag_input_relax" not found
by Wexter300 » Mon, 2023-01-23 11:32
4
139 by Wexter300
Wed, 2023-01-25 12:34
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
124 by JW_24
Tue, 2023-01-24 14:52
Normal topic Structure Prediction of protein mutant using relax
by Delfosse57 » Tue, 2023-01-10 13:26
1
152 by JW_24
Tue, 2023-01-24 04:55
Normal topic undefined symbol: ZN9CifString12UnknownValueE error meaning?
by aniyaz » Wed, 2023-01-04 08:37
3
246 by aniyaz
Wed, 2023-01-11 01:24
Normal topic Different dG_separated from RAbD and InterfaceAnalyzer
by brubin » Mon, 2022-12-19 13:58
2
290 by brubin
Tue, 2022-12-20 13:26
Normal topic Unexpected length of light chain FR1
by mgupta » Fri, 2022-12-09 01:03
0
288 by mgupta
Fri, 2022-12-09 01:03
Normal topic Prepacking crashing using metalloprotein
by mb0261 » Tue, 2022-12-06 10:16
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255 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
247 by JasonIsaac
Mon, 2022-12-05 18:57
Normal topic Adding NCAA with Metal Ion
by MustafaBughio » Mon, 2022-11-28 15:07
1
349 by JasonIsaac
Mon, 2022-12-05 18:41
Normal topic Predicting structure of protein after a few mutations
by Delfosse57 » Thu, 2022-12-01 20:40
0
259 by Delfosse57
Thu, 2022-12-01 20:40
Normal topic Loop modeling
by Robertofg » Tue, 2022-11-22 00:34
0
251 by Robertofg
Tue, 2022-11-22 00:34
Normal topic N-Terminal Galactose
by SebastianBB » Mon, 2022-11-21 08:33
0
199 by SebastianBB
Mon, 2022-11-21 08:33
Normal topic Error in rosetta_scripts.mpi.linuxgccrelease: double free or corruption (!prev): 0x0000000007697a90
by almeida85 » Thu, 2022-11-17 01:04
0
190 by almeida85
Thu, 2022-11-17 01:04
Normal topic Where is Sicdock application now? Can I find a substitute?
by JasonIsaac » Sun, 2022-11-13 03:41
3
305 by rmoretti
Mon, 2022-11-14 07:27
Normal topic pose.energies().total_enegies().show_nonzero() changes after packer is applied
by Liviu Copoiu » Mon, 2022-11-07 16:51
2
273 by Liviu Copoiu
Tue, 2022-11-08 10:43
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
403 by JasonIsaac
Mon, 2022-11-07 19:15
Normal topic Error with sequence_tolerance.R processing the checkpoint files, *.ga.entities and *.ga.generations.
by He Xiao » Mon, 2022-11-07 03:41
0
193 by He Xiao
Mon, 2022-11-07 04:10
Normal topic total_score changes when decomposing bb hbonds ref2015
by Liviu Copoiu » Mon, 2022-10-31 15:40
2
243 by Liviu Copoiu
Mon, 2022-10-31 16:03
Normal topic Failure to produce a cst file
by biotech » Wed, 2022-10-26 11:17
0
181 by biotech
Wed, 2022-10-26 11:17
Normal topic On iterations in ddg_monomer
by Proteinmechanic » Fri, 2022-09-30 21:23
0
189 by Proteinmechanic
Fri, 2022-09-30 21:23
Normal topic Save silent results to individual directory by process ID
by Payne » Sat, 2022-09-24 05:23
3
371 by rmoretti
Thu, 2022-09-29 00:15
Normal topic Ensemble Docking with RosettaDock 4.0 Protocol
by mb0261 » Wed, 2022-07-27 07:00
1
443 by mb0261
Mon, 2022-09-26 07:50
Normal topic GeneralizedKIC side chain closure.
by almeida85 » Mon, 2022-09-19 06:13
0
205 by almeida85
Mon, 2022-09-19 07:22
Normal topic Rosettascript - change residue number and chain ID
by cttm4a1 » Wed, 2022-09-14 23:40
0
185 by cttm4a1
Wed, 2022-09-14 23:40
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
229 by rmoretti
Wed, 2022-09-14 09:14
Normal topic Residue outside res_map range
by to-qinbin@163.com » Sat, 2022-09-10 01:56
1
376 by rmoretti
Mon, 2022-09-12 07:01
Normal topic clean_pdb_keep_ligand.py IndexError
by to-qinbin@163.com » Sat, 2022-09-10 04:04
1
253 by rmoretti
Mon, 2022-09-12 06:58
Normal topic Proper indexing of grafted residues by CCDEndsGraftMover
by cttm4a1 » Wed, 2022-09-07 23:41
0
180 by cttm4a1
Wed, 2022-09-07 23:41
Normal topic Sequence symmetry during FastDesign for repeat protein design
by cttm4a1 » Tue, 2022-09-06 21:02
1
248 by rmoretti
Wed, 2022-09-07 09:19
Normal topic Multiple Relax runnings
by mb0261 » Sat, 2022-08-27 05:42
1
279 by rmoretti
Tue, 2022-09-06 08:22
Normal topic PDB weird to PDB rosetta friendly
by jpfuenzalidawx » Fri, 2022-09-02 04:43
1
243 by rmoretti
Tue, 2022-09-06 08:13
Normal topic Residue outside res_map range
by amcallister » Fri, 2022-04-22 11:26
1
413 by aneeqh
Fri, 2022-09-02 13:36
Normal topic Get fasta from PDB script correction - Solved
by ialvy » Tue, 2022-08-30 00:00
0
209 by ialvy
Tue, 2022-08-30 00:00
Normal topic Using specific rotamers
by sahn97 » Fri, 2022-08-26 13:45
1
284 by rmoretti
Fri, 2022-08-26 14:51
Normal topic GeneralizedKIC disulfide closure
by Ken » Tue, 2022-08-16 13:32
2
364 by Ken
Wed, 2022-08-17 08:04
Normal topic Designing Feasible Backbones
by csvajda » Sat, 2022-08-13 08:08
0
229 by csvajda
Sat, 2022-08-13 08:08
Normal topic Unrecognized D-Leu name / C-terminal ACE
by almeida85 » Thu, 2022-08-11 07:43
1
290 by almeida85
Fri, 2022-08-12 05:56
Normal topic ERROR: Unable to open weights/patch file
by almeida85 » Tue, 2022-08-09 05:33
2
342 by almeida85
Thu, 2022-08-11 00:32
Normal topic Repeated entries in silent file
by almeida85 » Fri, 2022-08-05 02:52
4
534 by almeida85
Thu, 2022-08-11 00:29
Normal topic Interface scores comparison
by NingNing » Tue, 2022-08-09 17:36
0
197 by NingNing
Tue, 2022-08-09 17:36
Normal topic Problems with ICOOR when generating polymer params file
by liuwenxi » Tue, 2022-08-09 08:33
0
195 by liuwenxi
Tue, 2022-08-09 08:33
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
369 by rmoretti
Tue, 2022-08-09 06:52
Normal topic Temperature
by mrosam » Mon, 2022-08-08 01:37
0
192 by mrosam
Mon, 2022-08-08 01:37
Normal topic Renumbering PDB
by jgustat » Wed, 2022-07-27 13:37
2
420 by jgustat
Thu, 2022-07-28 10:00
Normal topic Applying dihedral constraints to TRP dipeptide minimization. ACE/NME termni.
by reoverstreet » Mon, 2022-07-11 14:39
1
397 by matteoferla
Wed, 2022-07-20 10:33
Normal topic XML schema file taken from Rosie docking giving errors in Rosetta Scripts
by Delfosse57 » Mon, 2022-07-18 10:51
3
521 by rmoretti
Mon, 2022-07-18 11:56
Normal topic Porblem with Rosetta Homology Modelling
by Karthik » Wed, 2022-07-13 23:45
0
235 by Karthik
Wed, 2022-07-13 23:45
Normal topic RosettaDock-4.0 score term
by Zjq1998 » Wed, 2022-06-29 22:07
3
718 by ssrb
Tue, 2022-07-05 11:07
Normal topic RifGen error on rosetta, "assertion failed", please help!
by guowuchen » Thu, 2022-05-05 06:20
1
614 by sia
Tue, 2022-07-05 05:47
Normal topic Problem with undetected lower and upper terminus variants for new polymer
by Martin Floor » Sat, 2022-06-11 06:51
5
878 by matteoferla
Fri, 2022-07-01 13:49
Normal topic Output and Input Tutorial
by jgustat » Fri, 2022-07-01 13:07
2
465 by jgustat
Fri, 2022-07-01 13:26
Normal topic De Novo backbone generation vs Rosetta Match for enzdes and ligand binding.
by csvajda » Thu, 2022-06-30 09:55
2
433 by csvajda
Thu, 2022-06-30 16:26
Normal topic How to add new Movers to Rosetta
by mb0261 » Thu, 2022-06-30 10:48
0
221 by mb0261
Thu, 2022-06-30 10:48
Normal topic Problem with 'AddEncounterConstraintMover'
by mb0261 » Tue, 2022-06-28 10:00
1
358 by rmoretti
Tue, 2022-06-28 11:06
Normal topic Rosetta-foldtree and docking
by tingting » Tue, 2022-03-15 22:49
5
940 by aastha.pal
Mon, 2022-06-27 09:55
Normal topic Antigen-antibody modeling
by aastha.pal » Mon, 2022-06-27 09:34
0
251 by aastha.pal
Mon, 2022-06-27 09:34
Normal topic protein binder interface design error
by guowuchen » Thu, 2022-06-23 04:43
0
309 by guowuchen
Thu, 2022-06-23 04:43
Normal topic genkic mover produced an unwanted HN - CA bond
by cttm4a1 » Mon, 2022-06-20 14:25
2
426 by cttm4a1
Mon, 2022-06-20 16:58
Normal topic Generate template parameter file for a polymer
by anarob » Fri, 2022-06-10 11:05
1
377 by matteoferla
Fri, 2022-06-17 10:38
Normal topic RosettaDock-3.2 output
by Zjq1998 » Wed, 2022-06-15 23:54
0
256 by Zjq1998
Wed, 2022-06-15 23:54
Normal topic mol2genparams.py script dependencies
by dhirajks » Wed, 2022-06-08 16:46
1
364 by matteoferla
Thu, 2022-06-09 14:41
Normal topic score.sc only shows total_score and with all zeros
by johnnytam100 » Mon, 2022-06-06 20:04
2
469 by johnnytam100
Tue, 2022-06-07 19:18
Normal topic The hbond for REF2015
by asbelx » Mon, 2022-06-06 06:07
2
563 by asbelx
Mon, 2022-06-06 23:15
Normal topic Rosetta for design of artifical metalloenzyme
by Delfosse57 » Thu, 2022-05-19 21:47
1
516 by matteoferla
Fri, 2022-06-03 01:09
Normal topic RNA update library
by Anne Klein » Mon, 2022-05-16 16:04
2
533 by Anne Klein
Tue, 2022-05-24 21:38
Normal topic ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)
by Ken » Mon, 2022-05-23 07:16
1
434 by ajasja
Mon, 2022-05-23 07:19
Normal topic -ignore_unrecognized_res doesn't work
by e3lm » Fri, 2022-05-06 14:47
2
570 by e3lm
Fri, 2022-05-06 16:10
Normal topic rosetta scripts to superimpose multiple segments
by rlwoltz » Fri, 2022-04-29 15:15
0
295 by rlwoltz
Fri, 2022-04-29 15:15
Normal topic Question about remodelling
by tonycheng1688 » Mon, 2022-04-25 13:51
0
292 by tonycheng1688
Mon, 2022-04-25 13:51
Normal topic Differentiable Energy Function w/ Centroid Representation
by protein_fan » Sun, 2022-03-20 09:39
4
885 by protein_fan
Fri, 2022-04-15 17:41
Normal topic InterfaceDdGMover and ResfileReader
by asaf.farhi » Wed, 2022-04-13 15:05
0
397 by asaf.farhi
Wed, 2022-04-13 15:05
Normal topic Error: Start tag expected, '<' not found
by Isomerase » Wed, 2022-04-06 19:45
1
752 by rmoretti
Thu, 2022-04-07 07:51
Normal topic Weekly releases for commercial users?
by rjacak » Tue, 2022-03-22 07:48
2
612 by rjacak
Thu, 2022-03-31 10:53
Normal topic RifDock building error on Ubuntu 20.04,please help!
by guowuchen » Mon, 2022-03-28 03:53
2
971 by guowuchen
Wed, 2022-03-30 04:20
Normal topic protein location change during Docking protocol
by Hyun » Tue, 2022-03-29 19:53
0
270 by Hyun
Tue, 2022-03-29 19:53
Normal topic Ensemble file required for both partners with docking prepack protocol
by katherinemccoy » Tue, 2022-03-29 14:26
0
300 by katherinemccoy
Tue, 2022-03-29 14:26
Normal topic abinitio demo is not progressing - new install
by jtpi6174 » Thu, 2022-03-24 03:49
2
665 by jtpi6174
Thu, 2022-03-24 09:43

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