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error in loop remodeling

Submitted by syntekabio2019 on Wed, 2023-04-05 01:00
Category: 
Loop Modeling

 

Hi I'm trying to fill the missing loop with remodel.linuxgccrelease in rosetta

for some pdb, there's no problem in filling missing loop

but I got following error with certain PDB

core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues.
core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLLL  |  aa = .......
core.fragment.picking_old.vall.eval.ABEGOEval: abego = LLLLLLL
core.sequence.ABEGOManager: [ ERROR ] Unrecognized abego index: L

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Rosetta 3 - Applications

Error with residue selectors not counting indices correctly.

Submitted by Wexter300 on Tue, 2023-04-04 11:04
Category: 
Design

I have a 4 chain, 96 residues long PDB file. all four chains are identical, so I set up my rosettascript with the following indices to select each chain to mutate them.

<Index name="chain1" resnums="1-24"/>

<Index name="chain2" resnums="24-48"/>

<Index name="chain3" resnums="48-72"/>

<Index name="chain4" resnums="72-96"/>

However I get the follwoing error message when running this script: 

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Rosetta 3 - General

Fork Rosetta for commercial license

Submitted by Pilyam on Mon, 2023-04-03 08:40
Category: 
Compilation

Hello,

My name is Or and I'm new to this forum so I appologise if my query is trivial or if this is not the right sub forum or category.

I work as a software developer at a company that uses Rosetta, we have a commertial licence. Sometimes, we change the CPP code, for example to add a new mover. 

We wish to create an inner github repo of Rosetta to keep track of our own changes.

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Rosetta 3 - Build/Install

Error with xml script

Submitted by almeida85 on Tue, 2023-03-28 01:53
Category: 
Non-Canonical Peptides

Hello,

I am using an xml script to design macrocycle peptides similar to https://www.pnas.org/doi/abs/10.1073/pnas.2012800118.

The script runs well in my HPC machine until it crashes unexpectedly. Attached is the output with the backtrace of the error. I am using Rosetta version rosetta.source.release-314 r314 2022.11+release.512e589 512e58946eaed9de20d65cdeea465e7690dc9e9a.

I am using the same script with a different peptide sequence and it runs well, until now.

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Rosetta 3 - Applications

Protein Protein Docking with Linker

Submitted by mrinal on Mon, 2023-03-20 15:58
Category: 
Loop Modeling

Hi

I am trying to dock to two proteins where the ends should be connected by a polyglycine linker. Is there a tutorial on protein protein docking constrained by a polyglycine linker. I would want to vary the linker and see the effect on the protein protein docking.

Mrinal

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Rosetta 3 - Applications

core.pose.util: (0) {0} [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

Submitted by ldx022 on Thu, 2023-03-16 04:13
Category: 
Design

Hello there,

I am trying to run a protocol published on nature protocols about "Modeling and docking of antibody structures with Rosetta".But when I run the application using the fasta sequence (shown as follows) provided in the article antibody,

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Rosetta 3 - Applications

Method for adding residues into PDB's w/ RosettaScripts.

Submitted by Wexter300 on Wed, 2023-03-15 13:07
Category: 
Design

I have been trying to insert residues into a PDB and then relaxing with Rosetta using rosettascripts. Currenlty I have managed a way to replace specified residues with another direct subsitution, but can;t figure out how to directly add more residues. I'm attempting another method by manually adding "dummy" residues into the pdb and then having rosetta replace those with the desired reisdue.  Would it be something accomplished using a resfile instead of a Rosettascripts function?

<ROSETTASCRIPTS>

<SCOREFXNS>

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Rosetta 3 - General

nvc++ error when compiling Rosetta for MPI on a supercomputer

Submitted by u.upadhyay on Wed, 2023-03-15 05:02
Category: 
Compilation

Hello everyone,

I have been working with Rosetta for the past year. I have installed and used it on multiple systems but recently I wanted to generate mass structures for many sequences. I got access to a supercomputer and want to use Rosetta, but I have been facing this problem where compilation with MPI support fails and gives an error for which I couldn't find a solution anywhere with a simple web search. 

If anyone else has faced this problem, I would really appreciate any help. Thanks.

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Rosetta 3 - Build/Install

scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_range_relax.mpi.linuxgccrelease] Error 1

Submitted by ldx022 on Sat, 2023-03-11 01:40
Category: 
Compilation

Hi there,

An attempt to compile rosetta using a later version of gcc (8.5.0) failed during compilation.(Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting. | RosettaCommons)

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Rosetta 3 - Build/Install

Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting.

Submitted by ldx022 on Thu, 2023-03-09 17:03
Category: 
Structure prediction

Hi there,

One problem with the initial use of antibody application is that there is complie issue shown as the following:

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Rosetta 3 - General

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