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Submitted by Sergey on Thu, 2011-02-03 09:58

When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

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PyRosetta - 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 - General

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

Extracting starting coordinates from ligand docking output

Submitted by rgb6@le.ac.uk on Wed, 2023-03-08 02:03
Category: 
Docking

I've done some ligand docking using cognate ligands, so used the starting coordinates of the input sdf file.  I now want to dock some analogues and want to use the same starting coordinates.  Is there a way to find what coordinates were used for the initial docking?

Thanks

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ROSIE - General

RuntimeError: CUDA out of memory.

Submitted by ravi.thakkar on Tue, 2023-03-07 00:27
Category: 
Compilation

I am having an error while running RFDiffusion.

I don't know where is the 

RuntimeError: CUDA out of memory. Tried to allocate 60.00 MiB (GPU 0; 1.95 GiB total capacity; 931.08 MiB already allocated; 25.00 MiB free; 984.00 MiB reserved in total by PyTorch)

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Rosetta 3 - General

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