diff --git a/Applications/AlphaFold/T1083_T1084.fasta b/Applications/AlphaFold/T1083_T1084.fasta new file mode 100644 index 0000000..b9351a0 --- /dev/null +++ b/Applications/AlphaFold/T1083_T1084.fasta @@ -0,0 +1,4 @@ +>T1083 +GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED +>T1084 +MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH diff --git a/Applications/AlphaFold/run_alphafold_multi.sh b/Applications/AlphaFold/run_alphafold_multi.sh new file mode 100644 index 0000000..f831c85 --- /dev/null +++ b/Applications/AlphaFold/run_alphafold_multi.sh @@ -0,0 +1,60 @@ +#!/bin/bash +#SBATCH -J AF_multimer # Job name +#SBATCH -p gpu # Partition(s) (separate with commas if using multiple) +#SBATCH --gres=gpu:1 # number of GPUs +#SBATCH -c 8 # Number of cores +#SBATCH -t 03:00:00 # Time (D-HH:MM:SS) +#SBATCH --mem=60G # Memory +#SBATCH -o AF_multi_%j.out # Name of standard output file +#SBATCH -e AF_multi_%j.err # Name of standard error file + +# set fasta file name +# NOTE: assumes this is in the directory you are running this script in +# note that you can run multiple proteins _sequentially_ (with the same model type) +# the names need to be provided as "protein1.fasta,protein2.fasta" +# if running multimer, provide one multifasta file +# indicate oligomeric state by including extra copies of a sequence +# they still require different _names_ though +my_fasta=T1083_T1084.fasta + +# set fasta-specific subfolder and filepath +# handling different possible .fasta suffixes +fasta_name="${my_fasta//.fasta}" +fasta_name="${fasta_name//.faa}" +fasta_name="${fasta_name//.fa}" +mkdir -p $fasta_name +cp $my_fasta $PWD/$fasta_name +my_fasta_path=$PWD/$fasta_name/$my_fasta + +# create and set path of output directory +my_output_dir=af2_out +mkdir -p $PWD/$fasta_name/$my_output_dir +my_output_dir_path=$PWD/$fasta_name/$my_output_dir + +# set model type (monomer, multimer, monomer_casp14, monomer_ptm) +# see notes under fasta file if running multimer +my_model_type=multimer + +# max pdb age +# use if you want to avoid recent templates +# format yyyy-mm-dd +my_max_date="2100-01-01" + +# run AlphaFold multimer using Singularity +singularity run --nv --env TF_FORCE_UNIFIED_MEMORY=1,XLA_PYTHON_CLIENT_MEM_FRACTION=4.0,OPENMM_CPU_THREADS=$SLURM_CPUS_PER_TASK,LD_LIBRARY_PATH=/usr/local/cuda-11.1/targets/x86_64-linux/lib/ --bind /n/holylfs04-ssd2/LABS/FAS/alphafold_database:/data -B .:/etc --pwd /app/alphafold /n/singularity_images/FAS/alphafold/alphafold_2.3.1.sif \ +--data_dir=/data/ \ +--bfd_database_path=/data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ +--db_preset=full_dbs \ +--fasta_paths=$my_fasta_path \ +--max_template_date=$my_max_date \ +--mgnify_database_path=/data/mgnify/mgy_clusters_2022_05.fa \ +--model_preset=$my_model_type \ +--obsolete_pdbs_path=/data/pdb_mmcif/obsolete.dat \ +--output_dir=$my_output_dir_path \ +--template_mmcif_dir=/data/pdb_mmcif/mmcif_files \ +--uniref30_database_path=/data/uniref30/UniRef30_2021_03 \ +--uniref90_database_path=/data/uniref90/uniref90.fasta \ +--pdb_seqres_database_path=/data/pdb_seqres/pdb_seqres.txt \ +--uniprot_database_path=/data/uniprot/uniprot.fasta \ +--use_gpu_relax=True +