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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. diff --git a/Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png b/Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png Binary files differnew file mode 100644 index 0000000..4b1bad2 --- /dev/null +++ b/Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png diff --git a/docs/feed.rss b/docs/feed.rss index 2cb2370..d4cd27c 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ <title>Navan's Archive</title> <description>Rare Tips, Tricks and Posts</description> <link>https://web.navan.dev/</link><language>en</language> - <lastBuildDate>Wed, 27 Mar 2024 23:45:05 -0000</lastBuildDate> - <pubDate>Wed, 27 Mar 2024 23:45:05 -0000</pubDate> + <lastBuildDate>Thu, 28 Mar 2024 21:27:46 -0000</lastBuildDate> + <pubDate>Thu, 28 Mar 2024 21:27:46 -0000</pubDate> <ttl>250</ttl> <atom:link href="https://web.navan.dev/feed.rss" rel="self" type="application/rss+xml"/> @@ -1955,6 +1955,414 @@ Serving HTTP on 0.0.0.0 port 8000 ... <item> <guid isPermaLink="true"> + https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html + </guid> + <title> + Fixing ADFRSuite for Apple Silicon + </title> + <description> + Fixing ADFRsuite on M1/MX chip Macs - CLI Tools + </description> + <link>https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html</link> + <pubDate>Thu, 28 Mar 2024 20:12:00 -0000</pubDate> + <content:encoded><![CDATA[<h1 id="fixing-adfrsuite-for-apple-silicon">Fixing ADFRSuite for Apple Silicon</h1> + +<p>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. </p> + +<p>These are the following issues that we will be fixing in this part:</p> + +<ul> +<li>“python2.7” cannot be opened because the developer cannot be verified.</li> +<li>OpenBabel Error</li> +<li>Segmentation fault while running the <a rel="noopener" target="_blank" href="https://ccsb.scripps.edu/adcp/tutorial-redocking/">redocking tutorial</a></li> +</ul> + +<p>For the sake of simplicity, I am assuming that I am running all these commands in the folder <code>~/Developer/scrippstuff/</code></p> + +<h2 id="installing-rosetta-2">Installing Rosetta 2</h2> + +<p>We are going to run all of these steps in the terminal</p> + +<div class="codehilite"> +<pre><span></span><code>/usr/sbin/softwareupdate<span class="w"> </span>--install-rosetta<span class="w"> </span>--agree-to-license +</code></pre> +</div> + +<h3 id="install-homebrew-for-x86">Install Homebrew for x86</h3> + +<p>Both versions of homebrew (x86 and arm64) can peacefully coexist on your system.</p> + +<p>From now on, every command should be run in a terminal session that starts with this as the first command:</p> + +<div class="codehilite"> +<pre><span></span><code>arch<span class="w"> </span>-x86_64<span class="w"> </span>zsh +</code></pre> +</div> + +<p>Now, we can install homebrew:</p> + +<div class="codehilite"> +<pre><span></span><code>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">"</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">"</span> +</code></pre> +</div> + +<p>Here is my output:</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>uname<span class="w"> </span>-a +Darwin<span class="w"> </span>Navans-MacBook-Pro.local<span class="w"> </span><span class="m">23</span>.3.0<span class="w"> </span>Darwin<span class="w"> </span>Kernel<span class="w"> </span>Version<span class="w"> </span><span class="m">23</span>.3.0:<span class="w"> </span>Wed<span class="w"> </span>Dec<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">21</span>:31:00<span class="w"> </span>PST<span class="w"> </span><span class="m">2023</span><span class="p">;</span><span class="w"> </span>root:xnu-10002.81.5~7/RELEASE_ARM64_T6020<span class="w"> </span>x86_64 +➜<span class="w"> </span>scrippstuff<span class="w"> </span>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">"</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">"</span> +<span class="o">==</span>><span class="w"> </span>Checking<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="sb">`</span>sudo<span class="sb">`</span><span class="w"> </span>access<span class="w"> </span><span class="o">(</span>which<span class="w"> </span>may<span class="w"> </span>request<span class="w"> </span>your<span class="w"> </span>password<span class="o">)</span>... +Password: +<span class="o">==</span>><span class="w"> </span>This<span class="w"> </span>script<span class="w"> </span>will<span class="w"> </span>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 +<span class="o">==</span>><span class="w"> </span>The<span class="w"> </span>following<span class="w"> </span>new<span class="w"> </span>directories<span class="w"> </span>will<span class="w"> </span>be<span class="w"> </span>created: +/usr/local/Cellar +/usr/local/Caskroom + +Press<span class="w"> </span>RETURN/ENTER<span class="w"> </span>to<span class="w"> </span><span class="k">continue</span><span class="w"> </span>or<span class="w"> </span>any<span class="w"> </span>other<span class="w"> </span>key<span class="w"> </span>to<span class="w"> </span>abort: +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/mkdir<span class="w"> </span>-p<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/chmod<span class="w"> </span><span class="nv">ug</span><span class="o">=</span>rwx<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>navanchauhan<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/bin/chgrp<span class="w"> </span>admin<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>-R<span class="w"> </span>navanchauhan:admin<span class="w"> </span>/usr/local/Homebrew +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/mkdir<span class="w"> </span>-p<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/chmod<span class="w"> </span>g+rwx<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>-R<span class="w"> </span>navanchauhan<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>and<span class="w"> </span>installing<span class="w"> </span>Homebrew... +remote:<span class="w"> </span>Enumerating<span class="w"> </span>objects:<span class="w"> </span><span class="m">47</span>,<span class="w"> </span><span class="k">done</span>. +remote:<span class="w"> </span>Counting<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">47</span>/47<span class="o">)</span>,<span class="w"> </span><span class="k">done</span>. +remote:<span class="w"> </span>Compressing<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">19</span>/19<span class="o">)</span>,<span class="w"> </span><span class="k">done</span>. +remote:<span class="w"> </span>Total<span class="w"> </span><span class="m">47</span><span class="w"> </span><span class="o">(</span>delta<span class="w"> </span><span class="m">28</span><span class="o">)</span>,<span class="w"> </span>reused<span class="w"> </span><span class="m">47</span><span class="w"> </span><span class="o">(</span>delta<span class="w"> </span><span class="m">28</span><span class="o">)</span>,<span class="w"> </span>pack-reused<span class="w"> </span><span class="m">0</span> +Unpacking<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">47</span>/47<span class="o">)</span>,<span class="w"> </span><span class="m">6</span>.11<span class="w"> </span>KiB<span class="w"> </span><span class="p">|</span><span class="w"> </span><span class="m">223</span>.00<span class="w"> </span>KiB/s,<span class="w"> </span><span class="k">done</span>. +From<span class="w"> </span>https://github.com/Homebrew/brew +<span class="w"> </span>+<span class="w"> </span>18ebdd8c8f...67a096fcbb<span class="w"> </span>tapioca-compiler-for-tty-rbi<span class="w"> </span>-><span class="w"> </span>origin/tapioca-compiler-for-tty-rbi<span class="w"> </span><span class="o">(</span>forced<span class="w"> </span>update<span class="o">)</span> +Switched<span class="w"> </span>to<span class="w"> </span>and<span class="w"> </span>reset<span class="w"> </span>branch<span class="w"> </span><span class="s1">'stable'</span> +<span class="o">==</span>><span class="w"> </span>Updating<span class="w"> </span>Homebrew... +<span class="o">==</span>><span class="w"> </span>Installation<span class="w"> </span>successful! + +<span class="o">==</span>><span class="w"> </span>Homebrew<span class="w"> </span>has<span class="w"> </span>enabled<span class="w"> </span>anonymous<span class="w"> </span>aggregate<span class="w"> </span>formulae<span class="w"> </span>and<span class="w"> </span>cask<span class="w"> </span>analytics. +Read<span class="w"> </span>the<span class="w"> </span>analytics<span class="w"> </span>documentation<span class="w"> </span><span class="o">(</span>and<span class="w"> </span>how<span class="w"> </span>to<span class="w"> </span>opt-out<span class="o">)</span><span class="w"> </span>here: +<span class="w"> </span>https://docs.brew.sh/Analytics +No<span class="w"> </span>analytics<span class="w"> </span>data<span class="w"> </span>has<span class="w"> </span>been<span class="w"> </span>sent<span class="w"> </span>yet<span class="w"> </span><span class="o">(</span>nor<span class="w"> </span>will<span class="w"> </span>any<span class="w"> </span>be<span class="w"> </span>during<span class="w"> </span>this<span class="w"> </span>install<span class="w"> </span>run<span class="o">)</span>. + +<span class="o">==</span>><span class="w"> </span>Homebrew<span class="w"> </span>is<span class="w"> </span>run<span class="w"> </span>entirely<span class="w"> </span>by<span class="w"> </span>unpaid<span class="w"> </span>volunteers.<span class="w"> </span>Please<span class="w"> </span>consider<span class="w"> </span>donating: +<span class="w"> </span>https://github.com/Homebrew/brew#donations + +<span class="o">==</span>><span class="w"> </span>Next<span class="w"> </span>steps: +-<span class="w"> </span>Run<span class="w"> </span>these<span class="w"> </span>two<span class="w"> </span>commands<span class="w"> </span><span class="k">in</span><span class="w"> </span>your<span class="w"> </span>terminal<span class="w"> </span>to<span class="w"> </span>add<span class="w"> </span>Homebrew<span class="w"> </span>to<span class="w"> </span>your<span class="w"> </span>PATH: +<span class="w"> </span><span class="o">(</span>echo<span class="p">;</span><span class="w"> </span><span class="nb">echo</span><span class="w"> </span><span class="s1">'eval "$(/usr/local/bin/brew shellenv)"'</span><span class="o">)</span><span class="w"> </span>>><span class="w"> </span>/Users/navanchauhan/.zprofile +<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">"</span><span class="k">$(</span>/usr/local/bin/brew<span class="w"> </span>shellenv<span class="k">)</span><span class="s2">"</span> +-<span class="w"> </span>Run<span class="w"> </span>brew<span class="w"> </span><span class="nb">help</span><span class="w"> </span>to<span class="w"> </span>get<span class="w"> </span>started +-<span class="w"> </span>Further<span class="w"> </span>documentation: +<span class="w"> </span>https://docs.brew.sh +</code></pre> +</div> + +<p>At this point, you don't need to edit your <code>zshrc</code> or <code>zsh_profile</code>.</p> + +<h3 id="install-pyenv">Install pyenv</h3> + +<p>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.</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>brew<span class="w"> </span>install<span class="w"> </span><span class="nv">pyenv</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>dependencies<span class="w"> </span><span class="k">for</span><span class="w"> </span>pyenv:<span class="w"> </span>m4,<span class="w"> </span>autoconf,<span class="w"> </span>ca-certificates,<span class="w"> </span>openssl@3,<span class="w"> </span>pkg-config<span class="w"> </span>and<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">m4</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">autoconf</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>ca-certificates +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>openssl@3 +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>pkg-config +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">pyenv</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>dependencies<span class="w"> </span><span class="k">for</span><span class="w"> </span>pyenv:<span class="w"> </span>m4,<span class="w"> </span>autoconf,<span class="w"> </span>ca-certificates,<span class="w"> </span>openssl@3,<span class="w"> </span>pkg-config<span class="w"> </span>and<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">m4</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>m4--1.4.19.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/m4/1.4.19:<span class="w"> </span><span class="m">13</span><span class="w"> </span>files,<span class="w"> </span><span class="m">739</span>.9KB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">autoconf</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>autoconf--2.72.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/autoconf/2.72:<span class="w"> </span><span class="m">71</span><span class="w"> </span>files,<span class="w"> </span><span class="m">3</span>.6MB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>ca-certificates +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>ca-certificates--2024-03-11.all.bottle.tar.gz +<span class="o">==</span>><span class="w"> </span>Regenerating<span class="w"> </span>CA<span class="w"> </span>certificate<span class="w"> </span>bundle<span class="w"> </span>from<span class="w"> </span>keychain,<span class="w"> </span>this<span class="w"> </span>may<span class="w"> </span>take<span class="w"> </span>a<span class="w"> </span><span class="k">while</span>... +🍺<span class="w"> </span>/usr/local/Cellar/ca-certificates/2024-03-11:<span class="w"> </span><span class="m">3</span><span class="w"> </span>files,<span class="w"> </span><span class="m">229</span>.6KB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>openssl@3 +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>openssl@3--3.2.1.sonoma.bottle.1.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/openssl@3/3.2.1:<span class="w"> </span><span class="m">6</span>,874<span class="w"> </span>files,<span class="w"> </span><span class="m">32</span>.5MB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>pkg-config +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>pkg-config--0.29.2_3.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/pkg-config/0.29.2_3:<span class="w"> </span><span class="m">11</span><span class="w"> </span>files,<span class="w"> </span><span class="m">656</span>.4KB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>readline--8.2.10.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/readline/8.2.10:<span class="w"> </span><span class="m">50</span><span class="w"> </span>files,<span class="w"> </span><span class="m">1</span>.7MB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span><span class="nv">pyenv</span> +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>pyenv--2.3.36.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/pyenv/2.3.36:<span class="w"> </span><span class="m">1</span>,158<span class="w"> </span>files,<span class="w"> </span><span class="m">3</span>.4MB +<span class="o">==</span>><span class="w"> </span>Running<span class="w"> </span><span class="sb">`</span>brew<span class="w"> </span>cleanup<span class="w"> </span>pyenv<span class="sb">`</span>... +Disable<span class="w"> </span>this<span class="w"> </span>behaviour<span class="w"> </span>by<span class="w"> </span>setting<span class="w"> </span>HOMEBREW_NO_INSTALL_CLEANUP. +Hide<span class="w"> </span>these<span class="w"> </span>hints<span class="w"> </span>with<span class="w"> </span>HOMEBREW_NO_ENV_HINTS<span class="w"> </span><span class="o">(</span>see<span class="w"> </span><span class="sb">`</span>man<span class="w"> </span>brew<span class="sb">`</span><span class="o">)</span>. +</code></pre> +</div> + +<p>And, build the last version of Python 2.7</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span><span class="nv">PYENV_ROOT</span><span class="o">=</span><span class="s2">"~/Developer/scrippstuff"</span><span class="w"> </span>pyenv<span class="w"> </span>install<span class="w"> </span><span class="m">2</span>.7.18 +python-build:<span class="w"> </span>use<span class="w"> </span>openssl<span class="w"> </span>from<span class="w"> </span>homebrew +python-build:<span class="w"> </span>use<span class="w"> </span>readline<span class="w"> </span>from<span class="w"> </span>homebrew +Downloading<span class="w"> </span>Python-2.7.18.tar.xz... +-><span class="w"> </span>https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz +Installing<span class="w"> </span>Python-2.7.18... +patching<span class="w"> </span>file<span class="w"> </span>configure +patching<span class="w"> </span>file<span class="w"> </span>configure.ac +patching<span class="w"> </span>file<span class="w"> </span>setup.py +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Mac/Tools/pythonw.c'</span> +patching<span class="w"> </span>file<span class="w"> </span>setup.py +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Doc/library/ctypes.rst'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Lib/test/test_str.py'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Lib/test/test_unicode.py'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/_ctypes.c'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/callproc.c'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/ctypes.h'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/callproc.c'</span> +patching<span class="w"> </span>file<span class="w"> </span>setup.py +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Mac/Modules/qt/setup.py'</span> +patching<span class="w"> </span>file<span class="w"> </span>setup.py +python-build:<span class="w"> </span>use<span class="w"> </span>readline<span class="w"> </span>from<span class="w"> </span>homebrew +python-build:<span class="w"> </span>use<span class="w"> </span>zlib<span class="w"> </span>from<span class="w"> </span>xcode<span class="w"> </span>sdk +Installed<span class="w"> </span>Python-2.7.18<span class="w"> </span>to<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18 +</code></pre> +</div> + +<p>Test the new installation:</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>~/Developer/scrippstuff/<span class="se">\~</span>/Developer/scrippstuff/versions/2.7.18/bin/python2.7 +Python<span class="w"> </span><span class="m">2</span>.7.18<span class="w"> </span><span class="o">(</span>default,<span class="w"> </span>Mar<span class="w"> </span><span class="m">28</span><span class="w"> </span><span class="m">2024</span>,<span class="w"> </span><span class="m">20</span>:47:13<span class="o">)</span> +<span class="o">[</span>GCC<span class="w"> </span>Apple<span class="w"> </span>LLVM<span class="w"> </span><span class="m">15</span>.0.0<span class="w"> </span><span class="o">(</span>clang-1500.1.0.2.5<span class="o">)]</span><span class="w"> </span>on<span class="w"> </span>darwin +Type<span class="w"> </span><span class="s2">"help"</span>,<span class="w"> </span><span class="s2">"copyright"</span>,<span class="w"> </span><span class="s2">"credits"</span><span class="w"> </span>or<span class="w"> </span><span class="s2">"license"</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>more<span class="w"> </span>information. +>>><span class="w"> </span>from<span class="w"> </span>random<span class="w"> </span>import<span class="w"> </span>randint +>>><span class="w"> </span>randint<span class="o">(</span><span class="m">0</span>,10<span class="o">)</span> +<span class="m">6</span> +>>><span class="w"> </span>exit<span class="o">()</span> +</code></pre> +</div> + +<p>Now, we can compress this newly created Python version into a <code>tar.gz</code> file to replace the one provided in ADFRsuite<em>x86</em>64Darwin_1.0.tar.gz. Don't forget the <code>.</code> at the end</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>tar<span class="w"> </span>-C<span class="w"> </span>./<span class="se">\~</span>/Developer/scrippstuff/versions/2.7.18<span class="w"> </span>-czf<span class="w"> </span>new.tar.gz<span class="w"> </span>. +</code></pre> +</div> + +<h2 id="install-adfrsuite">Install ADFRsuite</h2> + +<p>If you don't already have the tarball, you can download it by:</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>curl<span class="w"> </span>-o<span class="w"> </span>adfr.tar.gz<span class="w"> </span>https://ccsb.scripps.edu/adfr/download/1033/ +</code></pre> +</div> + +<p>Uncompress it</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>tar<span class="w"> </span>-xvzf<span class="w"> </span>adfr.tar.gz +</code></pre> +</div> + +<p>Replace the provided Python archive with the one we created:</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADFRsuite_x86_64Darwin_1.0 +$<span class="w"> </span>mv<span class="w"> </span>new.tar.gz<span class="w"> </span>Python2.7.tar.gz +</code></pre> +</div> + +<p>Note: For some reason simply copying it doesn't work and you need to use <code>mv</code></p> + +<p>Just to not mess with anything else, I will be installing everything in a folder called <code>clean_install</code></p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>mkdir<span class="w"> </span>clean_install +$<span class="w"> </span>./install.sh<span class="w"> </span>-d<span class="w"> </span>clean_install +... +<span class="w"> </span>ADFRsuite<span class="w"> </span>installation<span class="w"> </span>complete. +To<span class="w"> </span>run<span class="w"> </span>agfr,<span class="w"> </span>agfrgui,<span class="w"> </span>adfr,<span class="w"> </span>autosite,<span class="w"> </span>about,<span class="w"> </span>pythonsh<span class="w"> </span>scripts<span class="w"> </span>located<span class="w"> </span>at: +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin +add<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin<span class="w"> </span>to<span class="w"> </span>the<span class="w"> </span>path<span class="w"> </span>environment<span class="w"> </span>variable<span class="w"> </span><span class="k">in</span><span class="w"> </span>.cshrc<span class="w"> </span>or<span class="w"> </span>.bashrc: +.cshrc: +<span class="nb">set</span><span class="w"> </span><span class="nv">path</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin<span class="w"> </span><span class="nv">$path</span><span class="o">)</span> + +.bashrc: +<span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:<span class="nv">$PATH</span> +</code></pre> +</div> + +<p>Now, to test <code>agfr</code>, first run the command (replacing <code>navanchauhan</code> with yout username)</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:<span class="nv">$PATH</span> +$<span class="w"> </span>agfr +➜<span class="w"> </span>ADFRsuite_x86_64Darwin_1.0<span class="w"> </span><span class="nv">agfr</span> +<span class="o">==============================</span> +***<span class="w"> </span>Open<span class="w"> </span>Babel<span class="w"> </span>Error<span class="w"> </span><span class="k">in</span><span class="w"> </span>openLib +<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so<span class="w"> </span>did<span class="w"> </span>not<span class="w"> </span>load<span class="w"> </span>properly. +<span class="w"> </span>Error:<span class="w"> </span>dlopen<span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so,<span class="w"> </span>0x0009<span class="o">)</span>:<span class="w"> </span>Library<span class="w"> </span>not<span class="w"> </span>loaded:<span class="w"> </span>/opt/X11/lib/libcairo.2.dylib +<span class="w"> </span>Referenced<span class="w"> </span>from:<span class="w"> </span><24174F3E-2670-79AC-4F26-F8B49774194A><span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so +<span class="w"> </span>Reason:<span class="w"> </span>tried:<span class="w"> </span><span class="s1">'/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/local/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file,<span class="w"> </span>not<span class="w"> </span><span class="k">in</span><span class="w"> </span>dyld<span class="w"> </span>cache<span class="o">)</span> +<span class="o">==============================</span> +</code></pre> +</div> + +<h2 id="fixing-open-babel-error">Fixing <code>Open Babel Error</code></h2> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>brew<span class="w"> </span>install<span class="w"> </span>cairo +</code></pre> +</div> + +<h2 id="completing-the-re-docking-tutorial">Completing the re-docking tutorial</h2> + +<h3 id="dowbloading-the-dataset">Dowbloading the dataset</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>curl<span class="w"> </span>-o<span class="w"> </span>tutorial-data.zip<span class="w"> </span>https://ccsb.scripps.edu/adcp/download/1063/ +$<span class="w"> </span>unzip<span class="w"> </span>tutorial-data.zip +$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADCP_tutorial_data/3Q47 +</code></pre> +</div> + +<h3 id="conversion-to-pdbqt">Conversion to PDBQT</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>reduce<span class="w"> </span>3Q47_rec.pdb<span class="w"> </span>><span class="w"> </span>3Q47_recH.pdb +$<span class="w"> </span>reduce<span class="w"> </span>3Q47_pep.pdb<span class="w"> </span>><span class="w"> </span>3Q47_pepH.pdb +</code></pre> +</div> + +<h3 id="preparing-receptor">Preparing Receptor</h3> + +<pre><code>$ prepare_receptor -r 3Q47_recH.pdb +$ prepare_ligand -l 3Q47_pepH.pdb +</code></pre> + +<h3 id="generate-target-file">Generate Target File</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47 +➜<span class="w"> </span>3Q47<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47 +Traceback<span class="w"> </span><span class="o">(</span>most<span class="w"> </span>recent<span class="w"> </span>call<span class="w"> </span>last<span class="o">)</span>: +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">36</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFR.utils.runAGFR<span class="w"> </span>import<span class="w"> </span>runAGFR +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">41</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFR.utils.maps<span class="w"> </span>import<span class="w"> </span>flexResStr2flexRes +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">35</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFRcc.adfr<span class="w"> </span>import<span class="w"> </span>GridMap +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">34</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFRcc.adfr<span class="w"> </span>import<span class="w"> </span>Parameters +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">43</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>import<span class="w"> </span>ADFRcc.adfrcc<span class="w"> </span>as<span class="w"> </span>CPP +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">28</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span><span class="nv">_adfrcc</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>swig_import_helper<span class="o">()</span> +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">24</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span>swig_import_helper +<span class="w"> </span><span class="nv">_mod</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>imp.load_module<span class="o">(</span><span class="s1">'_adfrcc'</span>,<span class="w"> </span>fp,<span class="w"> </span>pathname,<span class="w"> </span>description<span class="o">)</span> +ImportError:<span class="w"> </span>dlopen<span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so,<span class="w"> </span>0x0002<span class="o">)</span>:<span class="w"> </span>Library<span class="w"> </span>not<span class="w"> </span>loaded:<span class="w"> </span>/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib +<span class="w"> </span>Referenced<span class="w"> </span>from:<span class="w"> </span><424BF61E-BF0F-351E-B546-E82EBBD8FBF5><span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so +<span class="w"> </span>Reason:<span class="w"> </span>tried:<span class="w"> </span><span class="s1">'/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/local/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file,<span class="w"> </span>not<span class="w"> </span><span class="k">in</span><span class="w"> </span>dyld<span class="w"> </span>cache<span class="o">)</span> +➜<span class="w"> </span>3Q47 +</code></pre> +</div> + +<p>Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the <code>libgomp.1.dylib</code>. 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.</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>../../ +$<span class="w"> </span><span class="nb">pwd</span> +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0 +$<span class="w"> </span>curl<span class="w"> </span>-L<span class="w"> </span>-H<span class="w"> </span><span class="s2">"Authorization: Bearer QQ=="</span><span class="w"> </span>-o<span class="w"> </span>gcc8amd64.tar.gz<span class="w"> </span>https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2 +$<span class="w"> </span>tar<span class="w"> </span>-xzf<span class="w"> </span>gcc8amd64.tar.gz +$<span class="w"> </span>cp<span class="w"> </span>-r<span class="w"> </span>gcc@8/8.5.0/lib/gcc/8/*<span class="w"> </span>clean_install/lib/ +</code></pre> +</div> + +<p>Now, we should be able to go back and run the target generation command:</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADCP_tutorial_data/3Q47 +$<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47 +<span class="c1">#################################################################</span> +<span class="c1"># If you used AGFR in your work, please cite: #</span> +<span class="c1"># #</span> +<span class="c1"># P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and #</span> +<span class="c1"># M.F. Sanner #</span> +<span class="c1"># AutoDockFR: Advances in Protein-Ligand Docking with #</span> +... +</code></pre> +</div> + +<h3 id="docking-peptide">Docking Peptide</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>adcp<span class="w"> </span>-t<span class="w"> </span>3Q47.trg<span class="w"> </span>-s<span class="w"> </span>npisdvd<span class="w"> </span>-N<span class="w"> </span><span class="m">20</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1000000</span><span class="w"> </span>-o<span class="w"> </span>3Q47_redocking<span class="w"> </span>-ref<span class="w"> </span>3Q47_pepH.pdb +</code></pre> +</div> + +<p>There you have it. Running ADCP on the newest macOS version against all odds.</p> + +<p>I haven't yet looked into fixing/patching <code>agfrgui</code> 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.</p> + +<p>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.</p> +]]></content:encoded> + </item> + + <item> + <guid isPermaLink="true"> https://web.navan.dev/posts/2022-11-07-a-new-method-to-blog.html </guid> <title> diff --git a/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png b/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png Binary files differnew file mode 100644 index 0000000..4b1bad2 --- /dev/null +++ b/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png diff --git a/docs/index.html b/docs/index.html index da5e542..7b1f66c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -88,6 +88,19 @@ lead.innerText = new_phrase; <h1>Recent Posts</h1> <ul> + <li><a href="/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html">Fixing ADFRSuite for Apple Silicon</a></li> + <ul> + <li>Fixing ADFRsuite on M1/MX chip Macs - CLI Tools</li> + <li>Published On: 2024-03-28 20:12</li> + <li>Tags: + + <a href='/tags/macOS.html'>macOS</a>, + + <a href='/tags/Cheminformatics.html'>Cheminformatics</a> + + </ul> + + <li><a href="/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html">Quadratic Formula Derivation</a></li> <ul> <li>Quick derivation of the quadratic equation by completing the square</li> @@ -142,19 +155,6 @@ lead.innerText = new_phrase; </ul> - <li><a href="/3D-Designs/2024-02-17-Can-Holder-Mountain-Bike.html">Bike Soda Can Holder</a></li> - <ul> - <li>Carry your favourite soda (or beer) can with you while you ride</li> - <li>Published On: 2024-02-17 18:42</li> - <li>Tags: - - <a href='/tags/Mountain Biking.html'>Mountain Biking</a>, - - <a href='/tags/OpenSCAD.html'>OpenSCAD</a> - - </ul> - - </ul> <b>For all posts go to <a href="/posts">Posts</a></b> diff --git a/docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html b/docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html new file mode 100644 index 0000000..5b59fa1 --- /dev/null +++ b/docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html @@ -0,0 +1,484 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta http-equiv="content-type" content="text/html; charset=utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1"> + <meta name="theme-color" content="#6a9fb5"> + + <title>Fixing ADFRSuite for Apple Silicon</title> + + <!-- + <link rel="stylesheet" href="https://unpkg.com/latex.css/style.min.css" /> + --> + + <link rel="stylesheet" href="/assets/c-hyde.css" /> + + <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=PT+Sans:400,400italic,700|Abril+Fatface"> + + <link rel="stylesheet" href="/assets/main.css" /> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + <meta name="og:site_name" content="Navan Chauhan" /> + <link rel="canonical" href="https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html" /> + <meta name="twitter:url" content="https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html" /> + <meta name="og:url" content="https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html" /> + <meta name="twitter:title" content="Fixing ADFRSuite for Apple Silicon" /> + <meta name="og:title" content="Fixing ADFRSuite for Apple Silicon" /> + <meta name="description" content="Fixing ADFRsuite on M1/MX chip Macs - CLI Tools" /> + <meta name="twitter:description" content="Fixing ADFRsuite on M1/MX chip Macs - CLI Tools" /> + <meta name="og:description" content="Fixing ADFRsuite on M1/MX chip Macs - CLI Tools" /> + <meta name="twitter:card" content="summary_large_image" /> + <meta name="viewport" content="width=device-width, initial-scale=1.0" /> + <link rel="shortcut icon" href="/images/favicon.png" type="image/png" /> + <link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan" /> + <meta name="twitter:image" content="https://web.navan.dev/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png" /> + <meta name="og:image" content="https://web.navan.dev/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png" /> + <meta name="google-site-verification" content="LVeSZxz-QskhbEjHxOi7-BM5dDxTg53x2TwrjFxfL0k" /> + <script data-goatcounter="https://navanchauhan.goatcounter.com/count" + async src="//gc.zgo.at/count.js"></script> + <script defer data-domain="web.navan.dev" src="https://plausible.io/js/plausible.js"></script> + <link rel="manifest" href="/manifest.json" /> + +</head> +<body class="theme-base-0d"> + <div class="sidebar"> + <div class="container sidebar-sticky"> + <div class="sidebar-about"> + <h1><a href="/">Navan</a></h1> + <p class="lead" id="random-lead">Alea iacta est.</p> + </div> + + <ul class="sidebar-nav"> + <li><a class="sidebar-nav-item" href="/about/">about/links</a></li> + <li><a class="sidebar-nav-item" href="/posts/">posts</a></li> + <li><a class="sidebar-nav-item" href="/3D-Designs/">3D designs</a></li> + <li><a class="sidebar-nav-item" href="/feed.rss">RSS Feed</a></li> + <li><a class="sidebar-nav-item" href="/colophon/">colophon</a></li> + </ul> + <div class="copyright"><p>© 2019-2024. Navan Chauhan <br> <a href="/feed.rss">RSS</a></p></div> + </div> +</div> + +<script> +let phrases = [ + "Something Funny", "Veni, vidi, vici", "Alea iacta est", "In vino veritas", "Acta, non verba", "Castigat ridendo mores", + "Cui bono?", "Memento vivere", "अहम् ब्रह्मास्मि", "अनुगच्छतु प्रवाहं", "चरन्मार्गान्विजानाति", "coq de cheval", "我愛啤酒" + ]; + +let new_phrase = phrases[Math.floor(Math.random()*phrases.length)]; + +let lead = document.getElementById("random-lead"); +lead.innerText = new_phrase; +</script> + <div class="content container"> + + <div class="post"> + <h1 id="fixing-adfrsuite-for-apple-silicon">Fixing ADFRSuite for Apple Silicon</h1> + +<p>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. </p> + +<p>These are the following issues that we will be fixing in this part:</p> + +<ul> +<li>“python2.7” cannot be opened because the developer cannot be verified.</li> +<li>OpenBabel Error</li> +<li>Segmentation fault while running the <a rel="noopener" target="_blank" href="https://ccsb.scripps.edu/adcp/tutorial-redocking/">redocking tutorial</a></li> +</ul> + +<p>For the sake of simplicity, I am assuming that I am running all these commands in the folder <code>~/Developer/scrippstuff/</code></p> + +<h2 id="installing-rosetta-2">Installing Rosetta 2</h2> + +<p>We are going to run all of these steps in the terminal</p> + +<div class="codehilite"> +<pre><span></span><code>/usr/sbin/softwareupdate<span class="w"> </span>--install-rosetta<span class="w"> </span>--agree-to-license +</code></pre> +</div> + +<h3 id="install-homebrew-for-x86">Install Homebrew for x86</h3> + +<p>Both versions of homebrew (x86 and arm64) can peacefully coexist on your system.</p> + +<p>From now on, every command should be run in a terminal session that starts with this as the first command:</p> + +<div class="codehilite"> +<pre><span></span><code>arch<span class="w"> </span>-x86_64<span class="w"> </span>zsh +</code></pre> +</div> + +<p>Now, we can install homebrew:</p> + +<div class="codehilite"> +<pre><span></span><code>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">"</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">"</span> +</code></pre> +</div> + +<p>Here is my output:</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>uname<span class="w"> </span>-a +Darwin<span class="w"> </span>Navans-MacBook-Pro.local<span class="w"> </span><span class="m">23</span>.3.0<span class="w"> </span>Darwin<span class="w"> </span>Kernel<span class="w"> </span>Version<span class="w"> </span><span class="m">23</span>.3.0:<span class="w"> </span>Wed<span class="w"> </span>Dec<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">21</span>:31:00<span class="w"> </span>PST<span class="w"> </span><span class="m">2023</span><span class="p">;</span><span class="w"> </span>root:xnu-10002.81.5~7/RELEASE_ARM64_T6020<span class="w"> </span>x86_64 +➜<span class="w"> </span>scrippstuff<span class="w"> </span>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">"</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">"</span> +<span class="o">==</span>><span class="w"> </span>Checking<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="sb">`</span>sudo<span class="sb">`</span><span class="w"> </span>access<span class="w"> </span><span class="o">(</span>which<span class="w"> </span>may<span class="w"> </span>request<span class="w"> </span>your<span class="w"> </span>password<span class="o">)</span>... +Password: +<span class="o">==</span>><span class="w"> </span>This<span class="w"> </span>script<span class="w"> </span>will<span class="w"> </span>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 +<span class="o">==</span>><span class="w"> </span>The<span class="w"> </span>following<span class="w"> </span>new<span class="w"> </span>directories<span class="w"> </span>will<span class="w"> </span>be<span class="w"> </span>created: +/usr/local/Cellar +/usr/local/Caskroom + +Press<span class="w"> </span>RETURN/ENTER<span class="w"> </span>to<span class="w"> </span><span class="k">continue</span><span class="w"> </span>or<span class="w"> </span>any<span class="w"> </span>other<span class="w"> </span>key<span class="w"> </span>to<span class="w"> </span>abort: +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/mkdir<span class="w"> </span>-p<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/chmod<span class="w"> </span><span class="nv">ug</span><span class="o">=</span>rwx<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>navanchauhan<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/bin/chgrp<span class="w"> </span>admin<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>-R<span class="w"> </span>navanchauhan:admin<span class="w"> </span>/usr/local/Homebrew +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/mkdir<span class="w"> </span>-p<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/chmod<span class="w"> </span>g+rwx<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew +<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>-R<span class="w"> </span>navanchauhan<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>and<span class="w"> </span>installing<span class="w"> </span>Homebrew... +remote:<span class="w"> </span>Enumerating<span class="w"> </span>objects:<span class="w"> </span><span class="m">47</span>,<span class="w"> </span><span class="k">done</span>. +remote:<span class="w"> </span>Counting<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">47</span>/47<span class="o">)</span>,<span class="w"> </span><span class="k">done</span>. +remote:<span class="w"> </span>Compressing<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">19</span>/19<span class="o">)</span>,<span class="w"> </span><span class="k">done</span>. +remote:<span class="w"> </span>Total<span class="w"> </span><span class="m">47</span><span class="w"> </span><span class="o">(</span>delta<span class="w"> </span><span class="m">28</span><span class="o">)</span>,<span class="w"> </span>reused<span class="w"> </span><span class="m">47</span><span class="w"> </span><span class="o">(</span>delta<span class="w"> </span><span class="m">28</span><span class="o">)</span>,<span class="w"> </span>pack-reused<span class="w"> </span><span class="m">0</span> +Unpacking<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">47</span>/47<span class="o">)</span>,<span class="w"> </span><span class="m">6</span>.11<span class="w"> </span>KiB<span class="w"> </span><span class="p">|</span><span class="w"> </span><span class="m">223</span>.00<span class="w"> </span>KiB/s,<span class="w"> </span><span class="k">done</span>. +From<span class="w"> </span>https://github.com/Homebrew/brew +<span class="w"> </span>+<span class="w"> </span>18ebdd8c8f...67a096fcbb<span class="w"> </span>tapioca-compiler-for-tty-rbi<span class="w"> </span>-><span class="w"> </span>origin/tapioca-compiler-for-tty-rbi<span class="w"> </span><span class="o">(</span>forced<span class="w"> </span>update<span class="o">)</span> +Switched<span class="w"> </span>to<span class="w"> </span>and<span class="w"> </span>reset<span class="w"> </span>branch<span class="w"> </span><span class="s1">'stable'</span> +<span class="o">==</span>><span class="w"> </span>Updating<span class="w"> </span>Homebrew... +<span class="o">==</span>><span class="w"> </span>Installation<span class="w"> </span>successful! + +<span class="o">==</span>><span class="w"> </span>Homebrew<span class="w"> </span>has<span class="w"> </span>enabled<span class="w"> </span>anonymous<span class="w"> </span>aggregate<span class="w"> </span>formulae<span class="w"> </span>and<span class="w"> </span>cask<span class="w"> </span>analytics. +Read<span class="w"> </span>the<span class="w"> </span>analytics<span class="w"> </span>documentation<span class="w"> </span><span class="o">(</span>and<span class="w"> </span>how<span class="w"> </span>to<span class="w"> </span>opt-out<span class="o">)</span><span class="w"> </span>here: +<span class="w"> </span>https://docs.brew.sh/Analytics +No<span class="w"> </span>analytics<span class="w"> </span>data<span class="w"> </span>has<span class="w"> </span>been<span class="w"> </span>sent<span class="w"> </span>yet<span class="w"> </span><span class="o">(</span>nor<span class="w"> </span>will<span class="w"> </span>any<span class="w"> </span>be<span class="w"> </span>during<span class="w"> </span>this<span class="w"> </span>install<span class="w"> </span>run<span class="o">)</span>. + +<span class="o">==</span>><span class="w"> </span>Homebrew<span class="w"> </span>is<span class="w"> </span>run<span class="w"> </span>entirely<span class="w"> </span>by<span class="w"> </span>unpaid<span class="w"> </span>volunteers.<span class="w"> </span>Please<span class="w"> </span>consider<span class="w"> </span>donating: +<span class="w"> </span>https://github.com/Homebrew/brew#donations + +<span class="o">==</span>><span class="w"> </span>Next<span class="w"> </span>steps: +-<span class="w"> </span>Run<span class="w"> </span>these<span class="w"> </span>two<span class="w"> </span>commands<span class="w"> </span><span class="k">in</span><span class="w"> </span>your<span class="w"> </span>terminal<span class="w"> </span>to<span class="w"> </span>add<span class="w"> </span>Homebrew<span class="w"> </span>to<span class="w"> </span>your<span class="w"> </span>PATH: +<span class="w"> </span><span class="o">(</span>echo<span class="p">;</span><span class="w"> </span><span class="nb">echo</span><span class="w"> </span><span class="s1">'eval "$(/usr/local/bin/brew shellenv)"'</span><span class="o">)</span><span class="w"> </span>>><span class="w"> </span>/Users/navanchauhan/.zprofile +<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">"</span><span class="k">$(</span>/usr/local/bin/brew<span class="w"> </span>shellenv<span class="k">)</span><span class="s2">"</span> +-<span class="w"> </span>Run<span class="w"> </span>brew<span class="w"> </span><span class="nb">help</span><span class="w"> </span>to<span class="w"> </span>get<span class="w"> </span>started +-<span class="w"> </span>Further<span class="w"> </span>documentation: +<span class="w"> </span>https://docs.brew.sh +</code></pre> +</div> + +<p>At this point, you don't need to edit your <code>zshrc</code> or <code>zsh_profile</code>.</p> + +<h3 id="install-pyenv">Install pyenv</h3> + +<p>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.</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>brew<span class="w"> </span>install<span class="w"> </span><span class="nv">pyenv</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>dependencies<span class="w"> </span><span class="k">for</span><span class="w"> </span>pyenv:<span class="w"> </span>m4,<span class="w"> </span>autoconf,<span class="w"> </span>ca-certificates,<span class="w"> </span>openssl@3,<span class="w"> </span>pkg-config<span class="w"> </span>and<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">m4</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">autoconf</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>ca-certificates +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>openssl@3 +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>pkg-config +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4 +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">pyenv</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba +<span class="c1">############################################################################################################################################################### 100.0%</span> +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>dependencies<span class="w"> </span><span class="k">for</span><span class="w"> </span>pyenv:<span class="w"> </span>m4,<span class="w"> </span>autoconf,<span class="w"> </span>ca-certificates,<span class="w"> </span>openssl@3,<span class="w"> </span>pkg-config<span class="w"> </span>and<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">m4</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>m4--1.4.19.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/m4/1.4.19:<span class="w"> </span><span class="m">13</span><span class="w"> </span>files,<span class="w"> </span><span class="m">739</span>.9KB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">autoconf</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>autoconf--2.72.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/autoconf/2.72:<span class="w"> </span><span class="m">71</span><span class="w"> </span>files,<span class="w"> </span><span class="m">3</span>.6MB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>ca-certificates +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>ca-certificates--2024-03-11.all.bottle.tar.gz +<span class="o">==</span>><span class="w"> </span>Regenerating<span class="w"> </span>CA<span class="w"> </span>certificate<span class="w"> </span>bundle<span class="w"> </span>from<span class="w"> </span>keychain,<span class="w"> </span>this<span class="w"> </span>may<span class="w"> </span>take<span class="w"> </span>a<span class="w"> </span><span class="k">while</span>... +🍺<span class="w"> </span>/usr/local/Cellar/ca-certificates/2024-03-11:<span class="w"> </span><span class="m">3</span><span class="w"> </span>files,<span class="w"> </span><span class="m">229</span>.6KB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>openssl@3 +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>openssl@3--3.2.1.sonoma.bottle.1.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/openssl@3/3.2.1:<span class="w"> </span><span class="m">6</span>,874<span class="w"> </span>files,<span class="w"> </span><span class="m">32</span>.5MB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>pkg-config +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>pkg-config--0.29.2_3.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/pkg-config/0.29.2_3:<span class="w"> </span><span class="m">11</span><span class="w"> </span>files,<span class="w"> </span><span class="m">656</span>.4KB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">readline</span> +<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>readline--8.2.10.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/readline/8.2.10:<span class="w"> </span><span class="m">50</span><span class="w"> </span>files,<span class="w"> </span><span class="m">1</span>.7MB +<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span><span class="nv">pyenv</span> +<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>pyenv--2.3.36.sonoma.bottle.tar.gz +🍺<span class="w"> </span>/usr/local/Cellar/pyenv/2.3.36:<span class="w"> </span><span class="m">1</span>,158<span class="w"> </span>files,<span class="w"> </span><span class="m">3</span>.4MB +<span class="o">==</span>><span class="w"> </span>Running<span class="w"> </span><span class="sb">`</span>brew<span class="w"> </span>cleanup<span class="w"> </span>pyenv<span class="sb">`</span>... +Disable<span class="w"> </span>this<span class="w"> </span>behaviour<span class="w"> </span>by<span class="w"> </span>setting<span class="w"> </span>HOMEBREW_NO_INSTALL_CLEANUP. +Hide<span class="w"> </span>these<span class="w"> </span>hints<span class="w"> </span>with<span class="w"> </span>HOMEBREW_NO_ENV_HINTS<span class="w"> </span><span class="o">(</span>see<span class="w"> </span><span class="sb">`</span>man<span class="w"> </span>brew<span class="sb">`</span><span class="o">)</span>. +</code></pre> +</div> + +<p>And, build the last version of Python 2.7</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span><span class="nv">PYENV_ROOT</span><span class="o">=</span><span class="s2">"~/Developer/scrippstuff"</span><span class="w"> </span>pyenv<span class="w"> </span>install<span class="w"> </span><span class="m">2</span>.7.18 +python-build:<span class="w"> </span>use<span class="w"> </span>openssl<span class="w"> </span>from<span class="w"> </span>homebrew +python-build:<span class="w"> </span>use<span class="w"> </span>readline<span class="w"> </span>from<span class="w"> </span>homebrew +Downloading<span class="w"> </span>Python-2.7.18.tar.xz... +-><span class="w"> </span>https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz +Installing<span class="w"> </span>Python-2.7.18... +patching<span class="w"> </span>file<span class="w"> </span>configure +patching<span class="w"> </span>file<span class="w"> </span>configure.ac +patching<span class="w"> </span>file<span class="w"> </span>setup.py +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Mac/Tools/pythonw.c'</span> +patching<span class="w"> </span>file<span class="w"> </span>setup.py +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Doc/library/ctypes.rst'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Lib/test/test_str.py'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Lib/test/test_unicode.py'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/_ctypes.c'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/callproc.c'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/ctypes.h'</span> +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/callproc.c'</span> +patching<span class="w"> </span>file<span class="w"> </span>setup.py +patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Mac/Modules/qt/setup.py'</span> +patching<span class="w"> </span>file<span class="w"> </span>setup.py +python-build:<span class="w"> </span>use<span class="w"> </span>readline<span class="w"> </span>from<span class="w"> </span>homebrew +python-build:<span class="w"> </span>use<span class="w"> </span>zlib<span class="w"> </span>from<span class="w"> </span>xcode<span class="w"> </span>sdk +Installed<span class="w"> </span>Python-2.7.18<span class="w"> </span>to<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18 +</code></pre> +</div> + +<p>Test the new installation:</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>~/Developer/scrippstuff/<span class="se">\~</span>/Developer/scrippstuff/versions/2.7.18/bin/python2.7 +Python<span class="w"> </span><span class="m">2</span>.7.18<span class="w"> </span><span class="o">(</span>default,<span class="w"> </span>Mar<span class="w"> </span><span class="m">28</span><span class="w"> </span><span class="m">2024</span>,<span class="w"> </span><span class="m">20</span>:47:13<span class="o">)</span> +<span class="o">[</span>GCC<span class="w"> </span>Apple<span class="w"> </span>LLVM<span class="w"> </span><span class="m">15</span>.0.0<span class="w"> </span><span class="o">(</span>clang-1500.1.0.2.5<span class="o">)]</span><span class="w"> </span>on<span class="w"> </span>darwin +Type<span class="w"> </span><span class="s2">"help"</span>,<span class="w"> </span><span class="s2">"copyright"</span>,<span class="w"> </span><span class="s2">"credits"</span><span class="w"> </span>or<span class="w"> </span><span class="s2">"license"</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>more<span class="w"> </span>information. +>>><span class="w"> </span>from<span class="w"> </span>random<span class="w"> </span>import<span class="w"> </span>randint +>>><span class="w"> </span>randint<span class="o">(</span><span class="m">0</span>,10<span class="o">)</span> +<span class="m">6</span> +>>><span class="w"> </span>exit<span class="o">()</span> +</code></pre> +</div> + +<p>Now, we can compress this newly created Python version into a <code>tar.gz</code> file to replace the one provided in ADFRsuite<em>x86</em>64Darwin_1.0.tar.gz. Don't forget the <code>.</code> at the end</p> + +<div class="codehilite"> +<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>tar<span class="w"> </span>-C<span class="w"> </span>./<span class="se">\~</span>/Developer/scrippstuff/versions/2.7.18<span class="w"> </span>-czf<span class="w"> </span>new.tar.gz<span class="w"> </span>. +</code></pre> +</div> + +<h2 id="install-adfrsuite">Install ADFRsuite</h2> + +<p>If you don't already have the tarball, you can download it by:</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>curl<span class="w"> </span>-o<span class="w"> </span>adfr.tar.gz<span class="w"> </span>https://ccsb.scripps.edu/adfr/download/1033/ +</code></pre> +</div> + +<p>Uncompress it</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>tar<span class="w"> </span>-xvzf<span class="w"> </span>adfr.tar.gz +</code></pre> +</div> + +<p>Replace the provided Python archive with the one we created:</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADFRsuite_x86_64Darwin_1.0 +$<span class="w"> </span>mv<span class="w"> </span>new.tar.gz<span class="w"> </span>Python2.7.tar.gz +</code></pre> +</div> + +<p>Note: For some reason simply copying it doesn't work and you need to use <code>mv</code></p> + +<p>Just to not mess with anything else, I will be installing everything in a folder called <code>clean_install</code></p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>mkdir<span class="w"> </span>clean_install +$<span class="w"> </span>./install.sh<span class="w"> </span>-d<span class="w"> </span>clean_install +... +<span class="w"> </span>ADFRsuite<span class="w"> </span>installation<span class="w"> </span>complete. +To<span class="w"> </span>run<span class="w"> </span>agfr,<span class="w"> </span>agfrgui,<span class="w"> </span>adfr,<span class="w"> </span>autosite,<span class="w"> </span>about,<span class="w"> </span>pythonsh<span class="w"> </span>scripts<span class="w"> </span>located<span class="w"> </span>at: +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin +add<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin<span class="w"> </span>to<span class="w"> </span>the<span class="w"> </span>path<span class="w"> </span>environment<span class="w"> </span>variable<span class="w"> </span><span class="k">in</span><span class="w"> </span>.cshrc<span class="w"> </span>or<span class="w"> </span>.bashrc: +.cshrc: +<span class="nb">set</span><span class="w"> </span><span class="nv">path</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin<span class="w"> </span><span class="nv">$path</span><span class="o">)</span> + +.bashrc: +<span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:<span class="nv">$PATH</span> +</code></pre> +</div> + +<p>Now, to test <code>agfr</code>, first run the command (replacing <code>navanchauhan</code> with yout username)</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:<span class="nv">$PATH</span> +$<span class="w"> </span>agfr +➜<span class="w"> </span>ADFRsuite_x86_64Darwin_1.0<span class="w"> </span><span class="nv">agfr</span> +<span class="o">==============================</span> +***<span class="w"> </span>Open<span class="w"> </span>Babel<span class="w"> </span>Error<span class="w"> </span><span class="k">in</span><span class="w"> </span>openLib +<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so<span class="w"> </span>did<span class="w"> </span>not<span class="w"> </span>load<span class="w"> </span>properly. +<span class="w"> </span>Error:<span class="w"> </span>dlopen<span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so,<span class="w"> </span>0x0009<span class="o">)</span>:<span class="w"> </span>Library<span class="w"> </span>not<span class="w"> </span>loaded:<span class="w"> </span>/opt/X11/lib/libcairo.2.dylib +<span class="w"> </span>Referenced<span class="w"> </span>from:<span class="w"> </span><24174F3E-2670-79AC-4F26-F8B49774194A><span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so +<span class="w"> </span>Reason:<span class="w"> </span>tried:<span class="w"> </span><span class="s1">'/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/local/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file,<span class="w"> </span>not<span class="w"> </span><span class="k">in</span><span class="w"> </span>dyld<span class="w"> </span>cache<span class="o">)</span> +<span class="o">==============================</span> +</code></pre> +</div> + +<h2 id="fixing-open-babel-error">Fixing <code>Open Babel Error</code></h2> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>brew<span class="w"> </span>install<span class="w"> </span>cairo +</code></pre> +</div> + +<h2 id="completing-the-re-docking-tutorial">Completing the re-docking tutorial</h2> + +<h3 id="dowbloading-the-dataset">Dowbloading the dataset</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>curl<span class="w"> </span>-o<span class="w"> </span>tutorial-data.zip<span class="w"> </span>https://ccsb.scripps.edu/adcp/download/1063/ +$<span class="w"> </span>unzip<span class="w"> </span>tutorial-data.zip +$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADCP_tutorial_data/3Q47 +</code></pre> +</div> + +<h3 id="conversion-to-pdbqt">Conversion to PDBQT</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>reduce<span class="w"> </span>3Q47_rec.pdb<span class="w"> </span>><span class="w"> </span>3Q47_recH.pdb +$<span class="w"> </span>reduce<span class="w"> </span>3Q47_pep.pdb<span class="w"> </span>><span class="w"> </span>3Q47_pepH.pdb +</code></pre> +</div> + +<h3 id="preparing-receptor">Preparing Receptor</h3> + +<pre><code>$ prepare_receptor -r 3Q47_recH.pdb +$ prepare_ligand -l 3Q47_pepH.pdb +</code></pre> + +<h3 id="generate-target-file">Generate Target File</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47 +➜<span class="w"> </span>3Q47<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47 +Traceback<span class="w"> </span><span class="o">(</span>most<span class="w"> </span>recent<span class="w"> </span>call<span class="w"> </span>last<span class="o">)</span>: +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">36</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFR.utils.runAGFR<span class="w"> </span>import<span class="w"> </span>runAGFR +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">41</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFR.utils.maps<span class="w"> </span>import<span class="w"> </span>flexResStr2flexRes +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">35</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFRcc.adfr<span class="w"> </span>import<span class="w"> </span>GridMap +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">34</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>from<span class="w"> </span>ADFRcc.adfr<span class="w"> </span>import<span class="w"> </span>Parameters +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">43</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span>import<span class="w"> </span>ADFRcc.adfrcc<span class="w"> </span>as<span class="w"> </span>CPP +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">28</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module> +<span class="w"> </span><span class="nv">_adfrcc</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>swig_import_helper<span class="o">()</span> +<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">24</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span>swig_import_helper +<span class="w"> </span><span class="nv">_mod</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>imp.load_module<span class="o">(</span><span class="s1">'_adfrcc'</span>,<span class="w"> </span>fp,<span class="w"> </span>pathname,<span class="w"> </span>description<span class="o">)</span> +ImportError:<span class="w"> </span>dlopen<span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so,<span class="w"> </span>0x0002<span class="o">)</span>:<span class="w"> </span>Library<span class="w"> </span>not<span class="w"> </span>loaded:<span class="w"> </span>/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib +<span class="w"> </span>Referenced<span class="w"> </span>from:<span class="w"> </span><424BF61E-BF0F-351E-B546-E82EBBD8FBF5><span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so +<span class="w"> </span>Reason:<span class="w"> </span>tried:<span class="w"> </span><span class="s1">'/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/local/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file,<span class="w"> </span>not<span class="w"> </span><span class="k">in</span><span class="w"> </span>dyld<span class="w"> </span>cache<span class="o">)</span> +➜<span class="w"> </span>3Q47 +</code></pre> +</div> + +<p>Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the <code>libgomp.1.dylib</code>. 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.</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>../../ +$<span class="w"> </span><span class="nb">pwd</span> +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0 +$<span class="w"> </span>curl<span class="w"> </span>-L<span class="w"> </span>-H<span class="w"> </span><span class="s2">"Authorization: Bearer QQ=="</span><span class="w"> </span>-o<span class="w"> </span>gcc8amd64.tar.gz<span class="w"> </span>https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2 +$<span class="w"> </span>tar<span class="w"> </span>-xzf<span class="w"> </span>gcc8amd64.tar.gz +$<span class="w"> </span>cp<span class="w"> </span>-r<span class="w"> </span>gcc@8/8.5.0/lib/gcc/8/*<span class="w"> </span>clean_install/lib/ +</code></pre> +</div> + +<p>Now, we should be able to go back and run the target generation command:</p> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADCP_tutorial_data/3Q47 +$<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47 +<span class="c1">#################################################################</span> +<span class="c1"># If you used AGFR in your work, please cite: #</span> +<span class="c1"># #</span> +<span class="c1"># P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and #</span> +<span class="c1"># M.F. Sanner #</span> +<span class="c1"># AutoDockFR: Advances in Protein-Ligand Docking with #</span> +... +</code></pre> +</div> + +<h3 id="docking-peptide">Docking Peptide</h3> + +<div class="codehilite"> +<pre><span></span><code>$<span class="w"> </span>adcp<span class="w"> </span>-t<span class="w"> </span>3Q47.trg<span class="w"> </span>-s<span class="w"> </span>npisdvd<span class="w"> </span>-N<span class="w"> </span><span class="m">20</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1000000</span><span class="w"> </span>-o<span class="w"> </span>3Q47_redocking<span class="w"> </span>-ref<span class="w"> </span>3Q47_pepH.pdb +</code></pre> +</div> + +<p>There you have it. Running ADCP on the newest macOS version against all odds.</p> + +<p>I haven't yet looked into fixing/patching <code>agfrgui</code> 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.</p> + +<p>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.</p> + + </div> + <blockquote>If you have scrolled this far, consider subscribing to my mailing list <a href="https://listmonk.navan.dev/subscription/form">here.</a> You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.</blockquote> + <script data-isso="https://comments.navan.dev/" + src="https://comments.navan.dev/js/embed.min.js"></script> + <section id="isso-thread"> + <noscript>Javascript needs to be activated to view comments.</noscript> + </section> + + </div> + <script src="assets/manup.min.js"></script> + <script src="/pwabuilder-sw-register.js"></script> +</body> +</html>
\ No newline at end of file diff --git a/docs/posts/index.html b/docs/posts/index.html index a64a79a..ef630d7 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -84,6 +84,19 @@ lead.innerText = new_phrase; <ul> + <li><a href="/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html">Fixing ADFRSuite for Apple Silicon</a></li> + <ul> + <li>Fixing ADFRsuite on M1/MX chip Macs - CLI Tools</li> + <li>Published On: 2024-03-28 20:12</li> + <li>Tags: + + <a href='/tags/macOS.html'>macOS</a>, + + <a href='/tags/Cheminformatics.html'>Cheminformatics</a> + + </ul> + + <li><a href="/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html">Quadratic Formula Derivation</a></li> <ul> <li>Quick derivation of the quadratic equation by completing the square</li> diff --git a/docs/tags/Cheminformatics.html b/docs/tags/Cheminformatics.html index c686c20..6a98f75 100644 --- a/docs/tags/Cheminformatics.html +++ b/docs/tags/Cheminformatics.html @@ -81,6 +81,19 @@ lead.innerText = new_phrase; <ul> + <li><a href="/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html">Fixing ADFRSuite for Apple Silicon</a></li> + <ul> + <li>Fixing ADFRsuite on M1/MX chip Macs - CLI Tools</li> + <li>Published On: 2024-03-28 20:12</li> + <li>Tags: + + <a href='/tags/macOS.html'>macOS</a>, + + <a href='/tags/Cheminformatics.html'>Cheminformatics</a> + + </ul> + + <li><a href="/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html">Cheminformatics on the Web (2021)</a></li> <ul> <li>Summarising Cheminformatics on the web in 2021.</li> diff --git a/docs/tags/macOS.html b/docs/tags/macOS.html index 1fa2569..124d64b 100644 --- a/docs/tags/macOS.html +++ b/docs/tags/macOS.html @@ -81,6 +81,19 @@ lead.innerText = new_phrase; <ul> + <li><a href="/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html">Fixing ADFRSuite for Apple Silicon</a></li> + <ul> + <li>Fixing ADFRsuite on M1/MX chip Macs - CLI Tools</li> + <li>Published On: 2024-03-28 20:12</li> + <li>Tags: + + <a href='/tags/macOS.html'>macOS</a>, + + <a href='/tags/Cheminformatics.html'>Cheminformatics</a> + + </ul> + + <li><a href="/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html">Cross-Compiling Hello World for DOS on macOS</a></li> <ul> <li>This goes through compiling Open Watcom 2 and creating simple hello-world exampls</li> |
