downloads/alphafold_monomer_2.1.2.sh
... ...
@@ -0,0 +1,20 @@
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+#!/bin/bash
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+
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+input=$1
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+
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+ALPHAFOLD_X=2.1.2
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+/programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \
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+ --data_dir=/programs/local/alphafold/ \
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+ --output_dir=$(pwd) \
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+ --fasta_paths=${input} \
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+ --max_template_date=2020-05-14 \
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+ --db_preset=full_dbs \
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+ --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
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+ --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
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+ --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \
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+ --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \
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+ --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \
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+ --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \
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+ --use_gpu_relax=True \
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+ --model_preset=monomer \
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+ --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70
downloads/alphafold_multimer_2.1.2.sh
... ...
@@ -0,0 +1,21 @@
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+#!/bin/bash
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+
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+input=$1
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+
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+ALPHAFOLD_X=2.1.2
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+/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \
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+ --data_dir=/programs/local/alphafold \
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+ --output_dir=$(pwd) \
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+ --fasta_paths=${input} \
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+ --max_template_date=2020-05-14 \
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+ --db_preset=full_dbs \
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+ --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
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+ --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
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+ --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \
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+ --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \
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+ --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \
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+ --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \
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+ --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \
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+ --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \
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+ --use_gpu_relax=True \
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+ --model_preset=multimer
examples/alphafold2.md
... ...
@@ -158,7 +158,7 @@ Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`,
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--pdb70_database_path=/programs/local/alphafold/pdb70/pdb70
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```
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-where test_monomer.fasta is
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+where the input fasta is
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```
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>T1083
... ...
@@ -185,7 +185,7 @@ GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAA
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--model_preset=multimer
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```
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-where test_multimer.fasta is
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+where the input multimer fasta is
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```
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>T1083
... ...
@@ -194,6 +194,12 @@ GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAA
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MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH
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```
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+You can download example scripts of the above here:
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+[alphafold_monomer_2.1.2.sh](downloads/alphafold_monomer_2.1.2.sh)
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+[alphafold_multimer_2.1.2.sh](downloads/alphafold_multimer_2.1.2.sh)
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+
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+
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+
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**Alphafold2 2.1.1**
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**Standard prediction example :**
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```