Add multimer example

Applications/AlphaFold/T1083_T1084.fasta

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+>T1083
+GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED
+>T1084
+MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH

Applications/AlphaFold/run_alphafold_multi.sh

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+#!/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
+