rosettafoldnaNA: rapidly produces 3D structure models with confidence estimates for protein-DNA and protein-RNA complexes, and for RNA tertiary structures.

References:

• Baek M et al.Accurate prediction of nucleic acid and protein-nucleic acid complexes using rosettafoldnaNA biorxiv biorxiv | 

• rosettafoldna Github:Github

• Module Name: rosettafoldna (see the modules page for more information)
• Since only the last step of rosettafoldna can use GPU, we strongly suggest to run the edited pipeline which was spited to part1(CPUs and memory heavy) and part2(GPU >V100), see the examples in interactive job.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=10 --mem=70G
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load rosettafoldna
[user@cn3144]$ mkdir /data/$USER/rosettafoldna_test/
[user@cn3144]$ cd /data/$USER/rosettafoldna_test/
[user@cn3144]$ cp -r ${ROSETTAFOLDNA_TEST_DATA:-none}/* .
[user@cn3144]$ tree rosettafoldna_test/
rosettafoldna_test/
├── protein.fa
└── RNA.fa

0 directories, 2 files

[user@cn3144]$ run_RF2NA_part1.sh test_o protein.fa R:RNA.fa
Running HHblits
Running PSIPRED
Running hhsearch
Running rMSA (lite)
Done with part1, please run part2 on GPU node (>= V100)

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=10g --gres=gpu:v100:1
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144]$ run_RF2NA_part2.sh test_o protein.fa R:RNA.fa
Running RoseTTAFold2NA to predict structures
Running on GPU
  msa[msa == "U"] = 30
           plddt    best
RECYCLE  0   0.874  -1.000
RECYCLE  1   0.892   0.874
RECYCLE  2   0.898   0.892
RECYCLE  3   0.899   0.898
RECYCLE  4   0.901   0.899
RECYCLE  5   0.902   0.901
RECYCLE  6   0.901   0.902
RECYCLE  7   0.902   0.902
RECYCLE  8   0.901   0.902
RECYCLE  9   0.901   0.902
Done2 with part2 (prediction)

Create a batch input file (e.g. rosettafoldna_1.sh) for first step. For example:

#!/bin/bash
set -e
module load rosettafoldna
cd /data/$USER/rosettafoldna_test/
cp -r ${ROSETTAFOLDNA_TEST_DATA:-none}/* .
run_RF2NA_part1.sh test_o protein.fa R:RNA.fa

Then create a batch input file (e.g. rosettafoldna_2.sh) for the second step. For example:

#!/bin/bash
set -e
module load rosettafoldna
cd /data/$USER/rosettafoldna_test/
run_RF2NA_part2.sh test_o protein.fa R:RNA.fa

Submit this job using the Slurm sbatch command.

[user@biowulf]$ sbatch --cpus-per-task=10 --mem=70g rosettafoldna_1.sh
1001
[user@biowulf]$ sbatch --dependency=afterany:1001 --cpus-per-task=2 \
                  --mem=10g --partition=gpu --gres=gpu:v100:1 rosettafoldna_2.sh
1002