You are here
Rosetta 3 - Applications
Log in to post new content in the forum.
Topic / Topic starter |
Replies | Views | Last post | |
|---|---|---|---|---|
|
latest version of rosetta unable to build models by pramod » Mon, 2014-11-03 11:31 |
1 |
2,445 |
by rmoretti Tue, 2014-11-04 10:33 |
|
|
Lammps or RosettaSurface by StevPChem » Fri, 2016-06-10 10:13 |
3 |
3,405 |
by Anpu Tue, 2018-09-25 18:53 |
|
|
kinematic loop modeling multiple input: possible? by a_s_a » Thu, 2011-05-12 09:33 |
2 |
2,985 |
by a_s_a Mon, 2014-04-21 06:47 |
|
|
KIC with fragments versus Next generation KIC by Loki01 » Fri, 2018-09-07 05:06 |
3 |
2,443 |
by smlewis Mon, 2018-09-10 11:48 |
|
|
KeyError: 'subject-id' in antibody modelling by bogac » Mon, 2017-03-06 02:00 |
2 |
2,581 |
by bogac Tue, 2017-03-07 02:11 |
|
|
kcenters_clustering_of_fragments by bjharris » Mon, 2019-07-01 16:16 |
1 |
1,198 |
by bjharris Wed, 2020-07-01 23:25 |
|
|
JobDistributor problem in antibody modeling by Wizard » Wed, 2015-04-22 00:35 |
2 |
2,951 |
by Wizard Sun, 2015-04-26 22:36 |
|
|
jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease by fradom » Mon, 2017-11-27 02:55 |
6 |
3,998 |
by fradom Tue, 2017-12-05 01:52 |
|
|
JD2 MPI by jrcf » Wed, 2015-10-28 14:45 |
1 |
2,001 |
by rmoretti Sat, 2015-10-31 08:57 |
|
|
Issues with modifying dock.xml for multiple ligand docking by DGR95 » Fri, 2021-05-14 12:51 |
0 |
534 |
by DGR95 Fri, 2021-05-14 12:51 |
|
|
issues about cstfile in RosettaMatch by Nicole Deng » Fri, 2020-12-18 05:44 |
3 |
1,854 |
by He Xiao Sun, 2021-04-11 19:29 |
|
|
Issue with Rosetta LinkResidues Script by adityapadhi » Wed, 2019-11-20 22:00 |
1 |
1,082 |
by JackMaguire Fri, 2019-11-22 13:45 |
|
|
Is there a way to restrict memory usage of ddg_monomer? by cossio » Fri, 2015-01-30 14:35 |
5 |
4,523 |
by rmoretti Mon, 2015-02-09 12:04 |
|
|
Is native.pdb necess for fragment_picker？ by ylwang » Thu, 2020-03-12 00:57 |
2 |
1,445 |
by ylwang Thu, 2020-03-12 20:42 |
|
|
Is it possible to restart the ddg_monomer.linuxgccrelease? by lanselibai » Mon, 2015-09-07 03:46 |
1 |
1,812 |
by rmoretti Wed, 2015-09-09 12:01 |
|
|
is it necessary to always run relax before any Rosetta by mainzer » Fri, 2019-04-12 01:35 |
1 |
1,555 |
by rmoretti Wed, 2019-07-10 09:47 |
|
|
interface_delta ligand_docking by Prasanth Kumar » Tue, 2013-06-18 08:37 |
1 |
2,360 |
by rmoretti Mon, 2014-04-21 06:48 |
|
|
InterfaceAnalyzer：“too many tries in fill_missing_atoms!” by mxp » Tue, 2019-08-06 00:41 |
8 |
4,973 |
by mxp Mon, 2019-08-12 18:42 |
|
|
InterfaceAnalyzer problem by almeida » Mon, 2014-03-03 14:56 |
3 |
4,371 |
by smlewis Fri, 2014-03-07 14:09 |
|
|
InterfaceAnalyzer dSasa calculation by mintseris » Wed, 2015-09-02 09:43 |
2 |
3,919 |
by jadolfbr Thu, 2015-09-03 16:18 |
|
|
InterfaceAnalyzer -resfile by gw » Wed, 2011-11-02 16:01 |
1 |
2,622 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
Interface Analyzer Segmentation Fault by h_trasatti » Tue, 2017-02-21 12:48 |
1 |
1,966 |
by smlewis Tue, 2017-02-21 14:10 |
|
|
Interesting scoring performance in flexpepdock against random peptides by ziqi1234 » Fri, 2017-12-08 07:52 |
0 |
905 |
by ziqi1234 Fri, 2017-12-08 07:52 |
|
|
Instructing design scripts to use noncanonical AA instead of canonical by zcrook » Tue, 2014-11-25 10:43 |
1 |
1,831 |
by rmoretti Wed, 2014-11-26 07:51 |
|
|
Inserting residues using RosettaRemodel by eleishaj » Tue, 2015-11-24 08:54 |
7 |
7,228 |
by eyong123 Wed, 2015-12-09 07:17 |
|
|
Input structure by Soler » Mon, 2020-09-28 13:18 |
1 |
818 |
by ssrb Tue, 2020-09-29 12:37 |
|
|
input file for loop modeling by Negarsardar » Tue, 2019-04-16 10:21 |
1 |
1,181 |
by rmoretti Tue, 2019-04-16 11:07 |
|
|
Incorrect Jump being set in RosettaScripts docking mover by weehee » Fri, 2012-06-08 10:23 |
6 |
6,880 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
Incorporating iron-sulfur cluster into ROSETTA applications by Derek Smith » Thu, 2014-08-14 23:12 |
1 |
2,351 |
by rmoretti Fri, 2014-08-15 08:06 |
|
|
Including waters in RosettaCM by ajkal » Thu, 2017-04-27 11:59 |
9 |
6,523 |
by rpavlov Tue, 2017-06-06 11:45 |
|
|
Including ab-initio predicted model in fragment library generation by ashu4487 » Thu, 2016-12-08 17:49 |
2 |
2,024 |
by ashu4487 Sun, 2016-12-11 19:03 |
|
|
Include MHC alpha helices in loop modelling protocol for pMHC complex by Roberto » Thu, 2022-08-04 07:22 |
0 |
421 |
by Roberto Thu, 2022-08-04 07:22 |
|
|
in silico affinity maturation design by jarod » Mon, 2013-05-20 02:07 |
11 |
11,149 |
by jarod Mon, 2014-04-21 06:47 |
|
|
Imitating induced fit protocol in SymDock2 without any symmetry constraints by chenna » Fri, 2020-02-14 01:35 |
2 |
1,495 |
by chenna Wed, 2020-03-04 03:24 |
|
|
IL-2 gets better binding with beta / gamma by tonycheng1688 » Wed, 2022-05-25 10:23 |
0 |
506 |
by tonycheng1688 Wed, 2022-05-25 10:23 |
|
|
If "clustering.py" can be used for PDBs contain two chains? by lanselibai » Wed, 2014-11-05 06:05 |
7 |
6,233 |
by lanselibai Tue, 2014-12-02 09:43 |
|
|
Idealize in Rosetta 3.3 by jadolfbr » Tue, 2011-12-06 11:59 |
2 |
2,864 |
by jadolfbr Mon, 2014-04-21 06:47 |
|
|
I need some help for using pHDock applications(histidine protonation / pH-dependent binding) by leygkn » Tue, 2020-09-22 18:40 |
1 |
886 |
by leygkn Tue, 2020-09-22 22:46 |
|
|
I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes by Wenithor » Thu, 2022-01-06 12:20 |
0 |
636 |
by Wenithor Thu, 2022-01-06 12:20 |
|
|
hybrid approach - comparative and ab initio modelling by eprates » Wed, 2019-03-20 11:58 |
1 |
1,169 |
by rmoretti Fri, 2019-03-29 09:45 |
|
|
hpatch commands and how to identify patches by Bianca Oliva » Thu, 2021-04-29 04:02 |
0 |
635 |
by Bianca Oliva Thu, 2021-04-29 04:02 |
|
|
How tu use Delta filter's relax_mover by pocin » Sun, 2017-02-19 05:21 |
3 |
2,743 |
by rmoretti Wed, 2017-03-01 13:10 |
|
|
How to write down a connection between ligand's atom and metal ion from enzyme? by Corvin » Mon, 2021-02-15 06:54 |
7 |
2,375 |
by aloshbau Mon, 2021-03-01 20:06 |
|
|
How to use Rosetta to DISCARD a protein-protein docking interface? by cossio » Tue, 2015-05-26 06:24 |
2 |
2,806 |
by rmoretti Sat, 2015-07-11 13:38 |
|
|
How to use MHC Epitope energy (mhc_epitope) to deimmunize a protein structure? by Sunyp_IM » Sun, 2020-11-08 08:07 |
5 |
2,158 |
by Brahm Yachnin Wed, 2020-11-18 17:21 |
|
|
How to use base_pair_constraint for RNA as a constraint term？ by yels » Sat, 2021-04-03 01:19 |
1 |
766 |
by everyday847 Sun, 2021-04-04 12:48 |
|
|
How to use -cst_fa_file and -relax:constrain_relax_to_native_coords at the same time by Anatol » Thu, 2012-11-29 14:12 |
11 |
9,406 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to specify only design surface residues and loops by RosettaScripts? by johnnytam100 » Sun, 2019-04-07 21:47 |
4 |
2,412 |
by johnnytam100 Wed, 2019-04-10 02:48 |
|
|
How to sort a Silent File based on RMSD by JadAbbass » Sun, 2013-08-04 14:40 |
2 |
3,129 |
by lanselibai Mon, 2014-10-06 15:30 |
|
|
How to select docked models by Sunyp_IM » Mon, 2020-06-22 00:50 |
1 |
855 |
by ssrb Mon, 2020-06-22 13:12 |
|
|
How to scan double mutations in RosettaScripts? by msardejani » Mon, 2016-12-12 16:52 |
2 |
2,100 |
by msardejani Mon, 2016-12-12 17:48 |
|
|
How to run partial_thread in RosettaCM when residure are more than 9999? by lanselibai » Mon, 2020-05-11 22:43 |
2 |
1,585 |
by lanselibai Tue, 2020-05-12 20:25 |
|
|
how to run my openmp programe in rosetta3.3? by lihowe » Mon, 2012-02-27 23:43 |
1 |
2,170 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
how to run ala_scan.xml by xinmiaohe » Mon, 2019-08-26 09:38 |
0 |
794 |
by xinmiaohe Mon, 2019-08-26 09:38 |
|
|
How to restart RASREC run by aep » Fri, 2016-07-01 04:39 |
2 |
2,050 |
by aep Fri, 2016-07-01 06:54 |
|
|
how to repacking loop while freezing other residues? by jfhuang » Wed, 2012-07-25 06:59 |
10 |
7,791 |
by jfhuang Mon, 2014-04-21 06:47 |
|
|
how to reconstruct the whole complex after symmetric docking by Anonymous » Tue, 2012-07-03 02:44 |
2 |
2,902 |
by felipet Wed, 2014-07-02 07:26 |
|
|
How to preserve ACE/NME termini? by nitroamos » Tue, 2018-05-22 13:07 |
3 |
3,048 |
by rmoretti Thu, 2018-06-28 12:44 |
|
|
how to pick fragments for a transmembrane protein by tevang » Mon, 2012-05-28 06:52 |
1 |
2,020 |
by tevang Mon, 2014-04-21 06:47 |
|
|
How to Perform point mutations with NCAA by Subhrodeep Saha » Tue, 2021-06-22 02:05 |
2 |
1,215 |
by dnamkr Fri, 2022-04-22 17:00 |
|
|
How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI by kingljy » Sun, 2017-09-24 18:37 |
3 |
3,030 |
by rmoretti Tue, 2017-10-10 09:58 |
|
|
How to output all iteration structures from ddg_monomer? by cossio » Fri, 2014-12-26 13:40 |
4 |
4,233 |
by cossio Mon, 2015-01-19 07:10 |
|
|
How to only constructure the tail conformation when using "FloppyTail.linuxgccrelease"? by lanselibai » Mon, 2014-10-13 10:26 |
5 |
4,845 |
by lanselibai Wed, 2014-10-15 03:52 |
|
|
How to model missing residues on a protein from multiple PDB files? by cossio » Fri, 2015-08-21 07:18 |
6 |
11,838 |
by rmoretti Fri, 2015-09-11 13:27 |
|
|
How to minimize the decoys obtained from backrub? by Vedasheersh » Wed, 2017-06-14 10:26 |
5 |
3,504 |
by SenyorDrew Fri, 2017-06-30 09:47 |
|
|
How to make new VALL database? by Danielsebas » Sun, 2019-09-08 02:16 |
2 |
2,034 |
by Danielsebas Wed, 2019-09-11 00:44 |
|
|
how to make "static" built binaries use multiple cpus like "mpi"? by Danielsebas » Wed, 2019-09-18 06:41 |
3 |
2,039 |
by rmoretti Wed, 2019-09-18 10:21 |
|
|
how to know the precedure of solving a actural bio problem? like interface design? by qq7678500549 » Thu, 2020-08-06 18:45 |
2 |
1,157 |
by qq7678500549 Sun, 2020-08-09 18:59 |
|
|
how to generate the whole molecule that contains all the symmetric chains by Sunyp_IM » Sun, 2017-12-10 19:43 |
0 |
997 |
by Sunyp_IM Sun, 2017-12-10 19:43 |
|
|
How to freeze ligand during FastRelax? by dnamkr » Thu, 2020-01-02 14:53 |
1 |
1,237 |
by aloshbau Fri, 2020-01-10 16:48 |
|
|
how to fix the ATP HETATM by using movemap or constraint file? by ziqi1234 » Mon, 2017-11-20 06:43 |
9 |
5,604 |
by ziqi1234 Wed, 2017-11-22 06:21 |
|
|
how to find help informations on rosetta_scripts in rosetta3.10 by xinmiaohe » Mon, 2019-08-26 14:48 |
5 |
2,436 |
by xinmiaohe Tue, 2019-08-27 08:37 |
|
|
How to find cluster core structure? by assignfit » Thu, 2012-03-29 20:35 |
7 |
6,374 |
by attesor Wed, 2017-06-14 07:32 |
|
|
How to estimate the effect of a mutation on the binding energy? by ltrabuco » Tue, 2011-02-15 08:02 |
4 |
4,830 |
by jadolfbr Mon, 2014-04-21 06:47 |
|
|
How to eliminate "NUL"s when scoring PDBs? by lanselibai » Tue, 2014-10-14 10:04 |
2 |
2,624 |
by lanselibai Fri, 2014-10-17 03:36 |
|
|
how to do alanine scanning by xinmiaohe » Mon, 2019-08-26 17:40 |
5 |
3,884 |
by xinmiaohe Fri, 2019-10-04 08:54 |
|
|
How to design the anitgen-antibody interface by Sunyp_IM » Tue, 2017-12-12 18:44 |
0 |
1,013 |
by Sunyp_IM Tue, 2017-12-12 18:44 |
|
|
How to define pi-pi stacking in cst file? by lzx32 » Mon, 2011-07-04 23:47 |
6 |
7,285 |
by lzx32 Mon, 2014-04-21 06:47 |
|
|
How to create a native file for Protein-Protein docking by Kotimedidhi » Fri, 2020-06-19 08:58 |
2 |
1,294 |
by Kotimedidhi Mon, 2020-06-22 16:19 |
|
|
How to correctly incorporate constraint information into ab initio structure prediction? by johnnytam100 » Tue, 2019-02-19 03:13 |
2 |
1,813 |
by johnnytam100 Fri, 2019-03-01 01:36 |
|
|
how to control alignment for energy_based_clustering by xfradera » Tue, 2023-02-28 10:13 |
0 |
1,507 |
by xfradera Tue, 2023-02-28 10:13 |
|
|
How to concatenate the 3-mer and 9-mer files for RosettaCM? by lanselibai » Fri, 2020-05-08 05:38 |
5 |
2,481 |
by danpf Tue, 2020-05-12 10:58 |
|
|
How to choose designed antibody by Sunyp_IM » Wed, 2020-06-24 10:06 |
6 |
2,843 |
by chandana Tue, 2022-08-09 20:27 |
|
|
How to change the axes of "-spin" in docking_protocol by Zehui Zhou » Mon, 2023-02-13 22:06 |
0 |
1,582 |
by Zehui Zhou Mon, 2023-02-13 22:06 |
|
|
How to calculate dG? by yperez » Mon, 2012-10-22 07:28 |
1 |
2,634 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"? by lanselibai » Sat, 2015-01-17 11:19 |
1 |
2,824 |
by lanselibai Wed, 2015-01-21 02:40 |
|
|
How to apply cartesian_ddg to multi-metric enzyme? by Wang Zhe » Wed, 2021-12-08 10:07 |
0 |
573 |
by Wang Zhe Wed, 2021-12-08 10:07 |
|
|
How to analyse multiple silent files from "Abinitiorelax" output to find best models? by Danielsebas » Tue, 2019-09-10 10:01 |
1 |
1,105 |
by smlewis Mon, 2019-09-16 12:22 |
|
|
How to add constrains to FlexPepDocking? by MajorID » Thu, 2011-06-02 11:00 |
2 |
2,891 |
by MajorID Mon, 2014-04-21 06:47 |
|
|
How to add additional rounds of design and optimization in Rosetta scripts? by Nicole Deng » Tue, 2020-11-03 19:05 |
2 |
1,082 |
by Nicole Deng Thu, 2020-11-05 03:04 |
|
|
How to add a residue to one chain of an existing structure? by sn » Mon, 2017-04-17 09:34 |
2 |
2,627 |
by sn Thu, 2017-04-20 21:43 |
|
|
how to "rescore" the models using lowest energy model from rosetta run as native, for RMSD vs Score plot? by Danielsebas » Tue, 2019-09-24 03:51 |
1 |
1,247 |
by smlewis Tue, 2019-09-24 12:43 |
|
|
how to generate Fragments using up to 2001 structures only by oppopomoz » Sat, 2015-07-25 00:43 |
1 |
1,794 |
by rmoretti Thu, 2015-08-06 08:57 |
|
|
How many iterations of remodel is enough? by daniloboskovic » Thu, 2020-07-16 08:07 |
0 |
608 |
by daniloboskovic Thu, 2020-07-16 08:14 |
|
|
How does the label in pdb files looks like when using ResiduePDBInfoHasLabel? by johnnytam100 » Fri, 2019-08-16 00:25 |
1 |
1,372 |
by JackMaguire Fri, 2019-08-16 07:41 |
|
|
How do you use two patches simulataneously with ab initio folding? by smiruthi » Wed, 2011-12-21 15:24 |
5 |
4,718 |
by wangyr Mon, 2014-04-21 06:47 |
|
|
How do I explicitly add residues for design in the interface optimization script? by ahonegger » Mon, 2014-05-12 07:40 |
2 |
3,082 |
by ahonegger Mon, 2014-05-12 09:08 |
|
|
How do I change the default Compiler for Rosetta？ by pagumaaaaa » Wed, 2022-03-16 00:23 |
2 |
859 |
by pagumaaaaa Thu, 2022-03-24 22:40 |
|
|
How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior ) by asbelx » Sat, 2019-06-08 00:07 |
3 |
2,021 |
by happycaapi Tue, 2021-06-29 15:35 |
|
|
How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"? by lanselibai » Tue, 2014-11-04 14:56 |
7 |
6,780 |
by lanselibai Wed, 2014-11-12 11:17 |
Log in to post new content in the forum.
