# Unsolved

The problem hasn't been solved

## Clustering problem

Category:
Scoring

Hi guys.

I met a problem when I was doing the clustering. I excuted this command but it was unexpectedly ended killed and had no result. I've 200 pdb files in this folder.

I'll be really grateful if it can be solved.

\$ /home/suuo/Rosetta/main/source/bin/cluster.default.linuxgccrelease -database /home/suuo/Rosetta/main/database -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out in:file:s *.pdb

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Category:
Docking

Hi Everyone,

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## multi ligand docking using rosetta script

Category:
Docking

Hi all.

I'm trying to dock  my ligand with HEM to CYP using rosetta script with XML protocol

overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and  ligand as separate entity

But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.

For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score

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## opencl support programs

Category:
Compilation

Hi, All:

We just compiled opencl version of rosetta. But when I run rosetta_scripts.opencl.linuxgccrelease, there is no running processes found in GPU. I am just wondering if GPU is supported after opencl version is successfully compiled. Thanks.

Best,

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## GeneralizedKIC loop closure error

Category:
Loop Modeling

Dear Rosetta Community,

I am trying to generate conformations for a 29 residue cyclic peptide with N-C terminal cyclisation. I've written a Rosetta Script that declares a bond between the N and C terminals and then performs a loop closure based on GeneralizedKIC.

However I am facing the following error:

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## Pyrosetta score protein structures with missing atoms in sidechain

Category:
PyRosetta

I have a question regarding Pyrosetta. Currently, I want to use pyrosetta to score some protein structures but with missing atoms in sidechain. So my protein structures contrain full-atoms for backbone but missing one or two atoms per residue on sidechain. I used pose_from_pdb to read my protein structure (pdb). But it seems pysoretta will fill in the missing atoms according to rotamer library. Is there a way to prevent it so I can just score my structures with missing atoms on sidechains?

Thanks a lot for the help,

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## Patch to impose tetrahedral geometry on backbone O atom

Category:
Non-Canonical Peptides

Hello,

I want to model the tetrahedral transition state of an enzyme where serine OG attacks the peptide backbone C atom. In this case the bond order of the backbone C=O bond changes to C-O(H) and the C-O(H) is not in plane anymore.

So far I wrote this patch file and added a hydrogen to the O atom in the input model which is named H01. The patch file is used since I get an error when I don't include it.

BEGIN_CASE

BEGIN_SELECTOR
NAME3 LEU
END_SELECTOR

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## Best way to store a pose by Pyrosetta for Pyrosetta

Category:
PyRosetta

A pose can have a constraint set, a modifiable residue set, an unnoticed pose.pdb_info().obsolete() == True case, virtual residues, energies and a few more. Therefore when saving to disk none of the following truly work as they save coordinates:

pose.dump_pdb('foo.pdb')
pose.dump_scored_pdb('foo.pdb', pyrosetta.get_fa_scorefxn())
pose.dump_cif('foo.cif')
pose.dump_mmtf('foo.mmtf')
pyrosetta.io.poses_to_silent([pose], 'foo.silent')

So I was hoping for an all-in-one

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## PDB Clustering

Category:
Scoring

Hello,

I was working on homology modeling and built 1000 models with ligands. I'm planning to select 100 top scored models and do clustering on them.

I tried cluster.linuxgccrelease, but the program didn't recognize the ligand. I specified the option -exclude_res, but it didn't work.

I also tried calibur.linuxgccrelease, but there are a lot of warnings instead of the output.

I'm attaching the log files. Can you help me with these issues? Thank you in advance!

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