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RosettaCM

Submitted by DmitriiN on Sun, 2017-01-22 17:52
Category: 
Structure prediction

Hello, everyone!

I have a question about the RosettaCM Monte-Carlo sampling. I know, that it is not a problem with a program, so it is not for forum, but I hope for the best!

In the article it is written that "A Monte Carlo trajectory is carried out with two types of moves. (1) Substitution of the backbone torsion angles of a randomly selected Rosetta de novo fragment for the current torsion angles of these residues, and regeneration of coordinates according to the fold tree". 

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Rosetta 3 - Applications

Error when running Remodel with EnzDes constraint file to extend c-terminal

Submitted by Jeffrey_Chen on Thu, 2017-01-19 06:20
Category: 
Design

hi, everybody

In my test in  running Remodel with EnzDes constraint file,

the blueprint file is:

''''
95 E .
96 F . CST1A 
97 S .
98 E L CST1B 
99 E L

#################

the cstfile is:

CST::BEGIN
  TEMPLATE::  ATOM_MAP: 1 atom_type: Nbb 
  TEMPLATE::  ATOM_MAP: 1 is_backbone
  TEMPLATE::  ATOM_MAP: 1 residue3:  ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN GLN ARG SER THR VAL TRP TYR

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Rosetta 3 - Applications

RosettaCM input file for running on Stampede

Submitted by smathersc on Wed, 2017-01-18 16:12
Category: 
Structure prediction

Hi,

I am trying to run RosettaCM on the Stampede supercomputer run by XSEDE from the University of Texas. I have not been able to figure out how to get the input file to work. I have used Stampede before but never with Rosettta. I have attached the file that I have currently been trying to use. If anyone has run Rosetta on Stampede (or any other computer using the slurm batch system), what is the input file that you use?

Thanks

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Rosetta 3 - Applications

Domain insertion with Non-CAA

Submitted by mwfranklin on Mon, 2017-01-16 12:30
Category: 
Design
Loop Modeling

Hi all,

I am trying to insert a long fragment (GFPStrand) into another protein (4e1s) using Remodel. I've delete the residues that were originally in 4e1s but left a few at the end as an anchor for the domain insertion. Remodel throws an error about insertion indices being 0 if I don't leave them to anchor it. Remodel accepts the domain insertion and starts on the loop closure. It also appears to close the loop, but then throws this error with trace: 

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Rosetta 3 - Applications

Different weights in the constraints for each stage of AbinitioRelax

Submitted by allan.ferrari on Sun, 2017-01-15 04:35
Category: 
Scoring

As each stage of AbInitio protocol call a different function (score0, score1, score2, score5 e score3), it appears to me that use a single cst_weight in my command line doesn't make sense (a single weight for every single stage). For that reason, I would like to test different weights for cst in each stage of Abinitio.

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Rosetta 3 - General

PocketGrid.cc file error during Rosetta compiling

Submitted by mwid on Wed, 2017-01-11 14:14
Category: 
Compilation

Hi,

I am trying to compile Rosetta 3.7 (Released Sep 11, 2016) and it was building fine until it hit this error (attached below). It seems to be upset about the PocketGrid.cc file, but I'm not sure how to go about solving the error since I'm not familiar with coding languages. Any help would be greatly appreciated. Thank you.

Marlyn

 

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Rosetta 3 - Build/Install

comparative modeling of a homodimer

Submitted by banshee on Mon, 2017-01-09 18:34
Category: 
Structure prediction

hello

i am trying to do comparative homology modeling of a dimer. does the input pdb have to have the dimer with both monomer threaded?

when i input a dimer pdb with grishin alignment file of the monomer i get a threaded pdb with only the monomer. can i use this pdb as the input pdb or do i need to thread the other monomer and add that to the input pdb? thanks!

oh and by the way is the robetta server down? thanks.

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Rosetta 3 - Applications

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