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shape complementarity

Category: 
Non-Canonical Peptides

I am using the shape complementarity filter to evaluate noncanonical amino acids. For several noncanonicals that contain Chlorine and Fluorine atoms the sc value is -1. I suspect this is due to the code for sc not being compatible with atom types that are not C,N,O,S,and P. Does anyone have a solution or suggestion on how to get sc updated to work with all NCAA's?

Post Situation: 

Error with RNA_denovo

Category: 
ROSIE

[START_BACKTRACE]: RAW_LIBC
/mnt/cidstore1/software/el7/rosetta/haswell/gcc62/3.13/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(backtrace_string(int)+0x3a) [0x7f2e28eff88a]
/mnt/cidstore1/software/el7/rosetta/haswell/gcc62/3.13/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x51) [0x7f2e28efee11]

Post Situation: 

Ligand Docking with ROSETTA

Category: 
Docking
Small Molecules

Hi,

I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:

1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.

2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.

3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).

Post Situation: 

Porblem with Rosetta Homology Modelling

Category: 
Structure prediction

I am facing SEGMENTATION FAULT error when I try to generate 10000 structures in Rosetta Homology modelling. I am running this through the Batch script. For example, when I give -out:nstruct 10000 in the flag file, it generates only 48 structures after that the job gets terminated. I have attached my batch script, flag file, Error file and the Rosettta_crash.log file here. Please, can anyone help me to find the solution to this problem? 

Flag File

Post Situation: 

Per residue total score

Category: 
Scoring

Hi Rosetta Team!

I read from the scoring tutorial this line

A rule of thumb: -1 to -3 REU per residue is typical while scoring a refined structure with ref2015 score function.

May I know if it is possible to directly call this per residue total score during scoring?

Thank you.

Post Situation: 

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