RF2NA

Summary

Sources: https://github.com/uw-ipd/RoseTTAFold2NA

License: MIT - academic use only.

Genetic Databases: /data/dustgroup/ReferenceData/rosettafold /data/dustgroup/ReferenceData/alphafold/ /software/rf2na/RoseTTAFold2NA/RNA/

Samples: /software/rf2na/RoseTTAFold2NA/example/

Sample Batch Script: /software/rf2na/RoseTTAFold2NA/example/sbatch_RF2NA.sh

casp14: https://www.predictioncenter.org/casp14/index.cgi (T1050)

RoseTTAFold2 protein/nucleic acid complex prediction

Running RF2NA

t000_/models/model_00.pdb

# Using the example:
cp -r /software/rf2na/RoseTTAFold/example .
# modify sbatch-RF2NA.sh as needed
sbatch sbatch-RF2NA.sh

The batch-script from the example folder:

#!/bin/bash
#SBATCH --partition=maxgpu,allgpu
#SBATCH --time=0-02:00:00
#SBATCH --constraint='V100|A100'
#SBATCH --output=rf2na-%j.out
unset LD_PRELOAD

#
#  setup
#
source /etc/profile.d/modules.sh
module load maxwell cuda/11.3 gcc/9.3

export PATH=/software/rf2na/bin:/software/rf2na/RoseTTAFold2NA:$PATH
. mamba-init
mamba activate rf2na

# makes sure installations in ~/.local don't get into the way
export PYTHONNOUSERSITE=1

CPU=$(( $(nproc) / 2 ))
MEM=$(( $(free -g | grep Mem: | awk '{print $2}') - 50 ))

# run the script
run_RF2NA.sh t000_ protein.fa R:RNA.fa
     

Result running the example