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examples/alphafold2.md
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3 | 3 | <!-- TOC --> |
4 | 4 | |
5 | 5 | - [ALPHAFOLD2](#alphafold2) |
6 | - - [Preparing to run Alphafold](#preparing-to-run-alphafold) |
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7 | - - [Running the python script run_alphafold.py](#running-the-python-script-run_alphafoldpy) |
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8 | - - [GPU Memory](#gpu-memory) |
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9 | - - [Web portal](#web-portal) |
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10 | - - [Changes in AlphaFold 2.1.1 multimer](#changes-in-alphafold-211-multimer) |
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11 | - - [Examples](#examples) |
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12 | - - [Known issues](#known-issues) |
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6 | + - [Preparing to run Alphafold](#preparing-to-run-alphafold) |
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7 | + - [Running the python script run_alphafold.py](#running-the-python-script-run_alphafoldpy) |
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8 | + - [GPU Memory](#gpu-memory) |
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9 | + - [Web portal](#web-portal) |
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10 | + - [Changes in AlphaFold 2.1.1 multimer](#changes-in-alphafold-211-multimer) |
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11 | + - [Examples](#examples) |
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12 | + - [Known issues](#known-issues) |
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13 | 13 | |
14 | 14 | <!-- /TOC --> |
15 | 15 | ### Preparing to run Alphafold |
... | ... | @@ -19,6 +19,11 @@ From the developers' original publication: "The provided inference script is opt |
19 | 19 | |
20 | 20 | The SBGrid installation of Alphafold2 does not require Docker to run, but does require a relatively recent NVidia GPU and updated driver. |
21 | 21 | |
22 | +**CUDA SDK is required** |
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23 | + |
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24 | +The alphafold2 pipeline requires that the [CUDA Toolkit](https://developer.nvidia.com/cuda-toolkit) SDK be installed. We use version 11.1 and have had success with latest versions. The executables provided in this package are not redistributable so we do not include them with our CUDA libraries. |
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25 | + |
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26 | +**Required Databases and Parameters** |
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22 | 27 | AlphaFold requires a set of (large) genetic databases that must be downloaded separately. See https://github.com/deepmind/alphafold#genetic-databases for more information. |
23 | 28 | |
24 | 29 | These databases can be downloaded with the included download script and the aria2c program, both of which are available in the SBGrid collection. Note that these databases are large in size (> 2Tb) and may require a significant amount of time to download. |
... | ... | @@ -110,7 +115,7 @@ To use it, set the ALPHAFOLD_X variable to 2.1.0 in the shell or in the ~/.sbgri |
110 | 115 | This is the standard SBGrid version override method. |
111 | 116 | |
112 | 117 | **NOTE** |
113 | -- Databases must be redownloaded, specifically UniProt and PDB seqres databases. |
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118 | +- Databases must be redownloaded for 2.1.1, specifically UniProt and PDB seqres databases. |
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114 | 119 | - Run `scripts/download_uniprot.sh <DOWNLOAD_DIR>`. |
115 | 120 | - Remove/rename `<DOWNLOAD_DIR>/pdb_mmcif`. It is needed to have PDB SeqRes and PDB from exactly the same date. Failure to do this step will result in potential errors when searching for templates when running AlphaFold-Multimer. |
116 | 121 | - Run `scripts/download_pdb_mmcif.sh <DOWNLOAD_DIR>`. |
... | ... | @@ -131,12 +136,12 @@ Some command line flags have changed since version 2.0.0. We recommend running t |
131 | 136 | --max_template_date=2020-05-14 \ |
132 | 137 | --db_preset=full_dbs \ |
133 | 138 | --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
134 | ---uniclust30_database_path=/programs/local/alphafold//uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
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135 | ---uniref90_database_path=/programs/local/alphafold//uniref90/uniref90.fasta \ |
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136 | ---mgnify_database_path=/programs/local/alphafold//mgnify/mgy_clusters_2018_12.fa \ |
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137 | ---template_mmcif_dir=/programs/local/alphafold//pdb_mmcif/mmcif_files \ |
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138 | ---pdb70_database_path=/programs/local/alphafold//pdb70/pdb70 \ |
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139 | ---obsolete_pdbs_path=/programs/local/alphafold//pdb_mmcif/obsolete.dat |
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139 | +--uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
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140 | +--uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
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141 | +--mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
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142 | +--template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
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143 | +--pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 \ |
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144 | +--obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat |
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140 | 145 | ``` |
141 | 146 | |
142 | 147 | where test_monomer.fasta is |