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diff --git a/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md b/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md new file mode 100644 index 0000000..f43f15c --- /dev/null +++ b/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md @@ -0,0 +1,379 @@ +--- +date: 2024-03-28 20:12 +description: Fixing ADFRsuite on M1/MX chip Macs - CLI Tools +tags: macOS, Cheminformatics +--- + +# Fixing ADFRSuite for Apple Silicon + +We are going to be running everything through Rosetta 2. I am confident that if I had access to the original source code, I could find a way to run everything natively. + +These are the following issues that we will be fixing in this part: + +* “python2.7” cannot be opened because the developer cannot be verified. +* OpenBabel Error +* Segmentation fault while running the [redocking tutorial](https://ccsb.scripps.edu/adcp/tutorial-redocking/) + +For the sake of simplicity, I am assuming that I am running all these commands in the folder `~/Developer/scrippstuff/` + +## Installing Rosetta 2 + +We are going to run all of these steps in the terminal + +```bash +/usr/sbin/softwareupdate --install-rosetta --agree-to-license +``` + +### Install Homebrew for x86 + +Both versions of homebrew (x86 and arm64) can peacefully coexist on your system. + +From now on, every command should be run in a terminal session that starts with this as the first command: + +```bash +arch -x86_64 zsh +``` + +Now, we can install homebrew: + +```bash +/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" +``` + +Here is my output: + +``` bash +➜ scrippstuff uname -a +Darwin Navans-MacBook-Pro.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:31:00 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6020 x86_64 +➜ scrippstuff /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" +==> Checking for `sudo` access (which may request your password)... +Password: +==> This script will install: +/usr/local/bin/brew +/usr/local/share/doc/homebrew +/usr/local/share/man/man1/brew.1 +/usr/local/share/zsh/site-functions/_brew +/usr/local/etc/bash_completion.d/brew +/usr/local/Homebrew +==> The following new directories will be created: +/usr/local/Cellar +/usr/local/Caskroom + +Press RETURN/ENTER to continue or any other key to abort: +==> /usr/bin/sudo /bin/mkdir -p /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /bin/chmod ug=rwx /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /usr/sbin/chown navanchauhan /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /usr/bin/chgrp admin /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan:admin /usr/local/Homebrew +==> /usr/bin/sudo /bin/mkdir -p /Users/navanchauhan/Library/Caches/Homebrew +==> /usr/bin/sudo /bin/chmod g+rwx /Users/navanchauhan/Library/Caches/Homebrew +==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan /Users/navanchauhan/Library/Caches/Homebrew +==> Downloading and installing Homebrew... +remote: Enumerating objects: 47, done. +remote: Counting objects: 100% (47/47), done. +remote: Compressing objects: 100% (19/19), done. +remote: Total 47 (delta 28), reused 47 (delta 28), pack-reused 0 +Unpacking objects: 100% (47/47), 6.11 KiB | 223.00 KiB/s, done. +From https://github.com/Homebrew/brew + + 18ebdd8c8f...67a096fcbb tapioca-compiler-for-tty-rbi -> origin/tapioca-compiler-for-tty-rbi (forced update) +Switched to and reset branch 'stable' +==> Updating Homebrew... +==> Installation successful! + +==> Homebrew has enabled anonymous aggregate formulae and cask analytics. +Read the analytics documentation (and how to opt-out) here: + https://docs.brew.sh/Analytics +No analytics data has been sent yet (nor will any be during this install run). + +==> Homebrew is run entirely by unpaid volunteers. Please consider donating: + https://github.com/Homebrew/brew#donations + +==> Next steps: +- Run these two commands in your terminal to add Homebrew to your PATH: + (echo; echo 'eval "$(/usr/local/bin/brew shellenv)"') >> /Users/navanchauhan/.zprofile + eval "$(/usr/local/bin/brew shellenv)" +- Run brew help to get started +- Further documentation: + https://docs.brew.sh +``` + +At this point, you don't need to edit your `zshrc` or `zsh_profile`. + +### Install pyenv + +The reason we are installing pyenv is because it is easier to build Python 2.7.18 from scratch than messing around with codesigning and quarantine bs on macOS. + +```bash +➜ scrippstuff brew install pyenv +==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36 +############################################################################################################################################################### 100.0% +==> Fetching dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline +==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +############################################################################################################################################################### 100.0% +==> Fetching m4 +==> Downloading https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76 +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +############################################################################################################################################################### 100.0% +==> Fetching autoconf +==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +############################################################################################################################################################### 100.0% +==> Fetching ca-certificates +==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +############################################################################################################################################################### 100.0% +==> Fetching openssl@3 +==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +############################################################################################################################################################### 100.0% +==> Fetching pkg-config +==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12 +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +############################################################################################################################################################### 100.0% +==> Fetching readline +==> Downloading https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4 +############################################################################################################################################################### 100.0% +==> Fetching pyenv +==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba +############################################################################################################################################################### 100.0% +==> Installing dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline +==> Installing pyenv dependency: m4 +==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json +==> Pouring m4--1.4.19.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/m4/1.4.19: 13 files, 739.9KB +==> Installing pyenv dependency: autoconf +==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json +==> Pouring autoconf--2.72.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/autoconf/2.72: 71 files, 3.6MB +==> Installing pyenv dependency: ca-certificates +==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json +==> Pouring ca-certificates--2024-03-11.all.bottle.tar.gz +==> Regenerating CA certificate bundle from keychain, this may take a while... +🍺 /usr/local/Cellar/ca-certificates/2024-03-11: 3 files, 229.6KB +==> Installing pyenv dependency: openssl@3 +==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json +==> Pouring openssl@3--3.2.1.sonoma.bottle.1.tar.gz +🍺 /usr/local/Cellar/openssl@3/3.2.1: 6,874 files, 32.5MB +==> Installing pyenv dependency: pkg-config +==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json +==> Pouring pkg-config--0.29.2_3.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/pkg-config/0.29.2_3: 11 files, 656.4KB +==> Installing pyenv dependency: readline +==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json +==> Pouring readline--8.2.10.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/readline/8.2.10: 50 files, 1.7MB +==> Installing pyenv +==> Pouring pyenv--2.3.36.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/pyenv/2.3.36: 1,158 files, 3.4MB +==> Running `brew cleanup pyenv`... +Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP. +Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`). +``` + +And, build the last version of Python 2.7 + +```bash +➜ scrippstuff PYENV_ROOT="~/Developer/scrippstuff" pyenv install 2.7.18 +python-build: use openssl from homebrew +python-build: use readline from homebrew +Downloading Python-2.7.18.tar.xz... +-> https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz +Installing Python-2.7.18... +patching file configure +patching file configure.ac +patching file setup.py +patching file 'Mac/Tools/pythonw.c' +patching file setup.py +patching file 'Doc/library/ctypes.rst' +patching file 'Lib/test/test_str.py' +patching file 'Lib/test/test_unicode.py' +patching file 'Modules/_ctypes/_ctypes.c' +patching file 'Modules/_ctypes/callproc.c' +patching file 'Modules/_ctypes/ctypes.h' +patching file 'Modules/_ctypes/callproc.c' +patching file setup.py +patching file 'Mac/Modules/qt/setup.py' +patching file setup.py +python-build: use readline from homebrew +python-build: use zlib from xcode sdk +Installed Python-2.7.18 to /Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18 +``` + +Test the new installation: + +```bash +➜ scrippstuff ~/Developer/scrippstuff/\~/Developer/scrippstuff/versions/2.7.18/bin/python2.7 +Python 2.7.18 (default, Mar 28 2024, 20:47:13) +[GCC Apple LLVM 15.0.0 (clang-1500.1.0.2.5)] on darwin +Type "help", "copyright", "credits" or "license" for more information. +>>> from random import randint +>>> randint(0,10) +6 +>>> exit() +``` + +Now, we can compress this newly created Python version into a `tar.gz` file to replace the one provided in ADFRsuite_x86_64Darwin_1.0.tar.gz. Don't forget the `.` at the end + +```bash +➜ scrippstuff tar -C ./\~/Developer/scrippstuff/versions/2.7.18 -czf new.tar.gz . +``` + +## Install ADFRsuite + +If you don't already have the tarball, you can download it by: + +```bash +$ curl -o adfr.tar.gz https://ccsb.scripps.edu/adfr/download/1033/ +``` + +Uncompress it + +```bash +$ tar -xvzf adfr.tar.gz +``` + +Replace the provided Python archive with the one we created: + +```bash +$ cd ADFRsuite_x86_64Darwin_1.0 +$ mv new.tar.gz Python2.7.tar.gz +``` + +Note: For some reason simply copying it doesn't work and you need to use `mv` + +Just to not mess with anything else, I will be installing everything in a folder called `clean_install` + +```bash +$ mkdir clean_install +$ ./install.sh -d clean_install +... + ADFRsuite installation complete. +To run agfr, agfrgui, adfr, autosite, about, pythonsh scripts located at: +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin +add /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin to the path environment variable in .cshrc or .bashrc: +.cshrc: +set path = (/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin $path) + +.bashrc: +export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH +``` + +Now, to test `agfr`, first run the command (replacing `navanchauhan` with yout username) + +```bash +$ export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH +$ agfr +➜ ADFRsuite_x86_64Darwin_1.0 agfr +============================== +*** Open Babel Error in openLib + /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so did not load properly. + Error: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so, 0x0009): Library not loaded: /opt/X11/lib/libcairo.2.dylib + Referenced from: <24174F3E-2670-79AC-4F26-F8B49774194A> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so + Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/usr/local/lib/libcairo.2.dylib' (no such file), '/usr/lib/libcairo.2.dylib' (no such file, not in dyld cache) +============================== +``` + + +## Fixing `Open Babel Error` + +```bash +$ brew install cairo +``` + +## Completing the re-docking tutorial + +### Dowbloading the dataset + +```bash +$ curl -o tutorial-data.zip https://ccsb.scripps.edu/adcp/download/1063/ +$ unzip tutorial-data.zip +$ cd ADCP_tutorial_data/3Q47 +``` + +### Conversion to PDBQT + +```bash +$ reduce 3Q47_rec.pdb > 3Q47_recH.pdb +$ reduce 3Q47_pep.pdb > 3Q47_pepH.pdb +``` + +### Preparing Receptor + +``` +$ prepare_receptor -r 3Q47_recH.pdb +$ prepare_ligand -l 3Q47_pepH.pdb +``` + +### Generate Target File + +```bash +$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 +➜ 3Q47 agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 +Traceback (most recent call last): + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py", line 36, in <module> + from ADFR.utils.runAGFR import runAGFR + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py", line 41, in <module> + from ADFR.utils.maps import flexResStr2flexRes + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py", line 35, in <module> + from ADFRcc.adfr import GridMap + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py", line 34, in <module> + from ADFRcc.adfr import Parameters + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py", line 43, in <module> + import ADFRcc.adfrcc as CPP + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 28, in <module> + _adfrcc = swig_import_helper() + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 24, in swig_import_helper + _mod = imp.load_module('_adfrcc', fp, pathname, description) +ImportError: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so, 0x0002): Library not loaded: /Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib + Referenced from: <424BF61E-BF0F-351E-B546-E82EBBD8FBF5> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so + Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache) +➜ 3Q47 +``` + +Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the `libgomp.1.dylib`. I haven't tested using a newer version of GCC to make it work. Building GCC 8 yourself is absolutely painful. We are going to use a copy generated by the homebrew team. + +```bash +$ cd ../../ +$ pwd +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0 +$ curl -L -H "Authorization: Bearer QQ==" -o gcc8amd64.tar.gz https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2 +$ tar -xzf gcc8amd64.tar.gz +$ cp -r gcc@8/8.5.0/lib/gcc/8/* clean_install/lib/ +``` + +Now, we should be able to go back and run the target generation command: + +```bash +$ cd ADCP_tutorial_data/3Q47 +$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 +################################################################# +# If you used AGFR in your work, please cite: # +# # +# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and # +# M.F. Sanner # +# AutoDockFR: Advances in Protein-Ligand Docking with # +... +``` + +### Docking Peptide + +```bash +$ adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb +``` + +There you have it. Running ADCP on the newest macOS version against all odds. + +I haven't yet looked into fixing/patching `agfrgui` as I don't use the software. But, if someone reallllly needs to run it on Apple Silicon, I am happy to take a look at monkeypatching it. + +In case years down the line the prebuilt version of GCC 8 is not available, let me know so I can replace the link with my mirror. |