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authorNavan Chauhan <navanchauhan@gmail.com>2024-03-28 21:28:46 -0600
committerNavan Chauhan <navanchauhan@gmail.com>2024-03-28 21:28:46 -0600
commitfdf67099dbe882b50444a42e4bbd024394cfb548 (patch)
treeac995c4baab0f69b558fbcc4baa3916b26dbcf5a
parent64f80f9211b97812e8552546b0c97c5bdb1e3328 (diff)
adfrsuite
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+---
+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
new file mode 100644
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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">&quot;</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">&quot;</span>
+</code></pre>
+</div>
+
+<p>Here is my output:</p>
+
+<div class="codehilite">
+<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>uname<span class="w"> </span>-a
+Darwin<span class="w"> </span>Navans-MacBook-Pro.local<span class="w"> </span><span class="m">23</span>.3.0<span class="w"> </span>Darwin<span class="w"> </span>Kernel<span class="w"> </span>Version<span class="w"> </span><span class="m">23</span>.3.0:<span class="w"> </span>Wed<span class="w"> </span>Dec<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">21</span>:31:00<span class="w"> </span>PST<span class="w"> </span><span class="m">2023</span><span class="p">;</span><span class="w"> </span>root:xnu-10002.81.5~7/RELEASE_ARM64_T6020<span class="w"> </span>x86_64
+➜<span class="w"> </span>scrippstuff<span class="w"> </span>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">&quot;</span><span class="k">$(</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">&quot;</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>-&gt;<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">&#39;stable&#39;</span>
+<span class="o">==</span>&gt;<span class="w"> </span>Updating<span class="w"> </span>Homebrew...
+<span class="o">==</span>&gt;<span class="w"> </span>Installation<span class="w"> </span>successful!
+
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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">&#39;eval &quot;$(/usr/local/bin/brew shellenv)&quot;&#39;</span><span class="o">)</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>/Users/navanchauhan/.zprofile
+<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">&quot;</span><span class="k">$(</span>/usr/local/bin/brew<span class="w"> </span>shellenv<span class="k">)</span><span class="s2">&quot;</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>&gt;<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>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">m4</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">autoconf</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span>ca-certificates
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span>openssl@3
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span>pkg-config
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">readline</span>
+<span class="o">==</span>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">pyenv</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Pouring<span class="w"> </span>ca-certificates--2024-03-11.all.bottle.tar.gz
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Installing<span class="w"> </span><span class="nv">pyenv</span>
+<span class="o">==</span>&gt;<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>&gt;<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">&quot;~/Developer/scrippstuff&quot;</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...
+-&gt;<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">&#39;Mac/Tools/pythonw.c&#39;</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">&#39;Doc/library/ctypes.rst&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Lib/test/test_str.py&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Lib/test/test_unicode.py&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/_ctypes.c&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/callproc.c&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/ctypes.h&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/callproc.c&#39;</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">&#39;Mac/Modules/qt/setup.py&#39;</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">&quot;help&quot;</span>,<span class="w"> </span><span class="s2">&quot;copyright&quot;</span>,<span class="w"> </span><span class="s2">&quot;credits&quot;</span><span class="w"> </span>or<span class="w"> </span><span class="s2">&quot;license&quot;</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>more<span class="w"> </span>information.
+&gt;&gt;&gt;<span class="w"> </span>from<span class="w"> </span>random<span class="w"> </span>import<span class="w"> </span>randint
+&gt;&gt;&gt;<span class="w"> </span>randint<span class="o">(</span><span class="m">0</span>,10<span class="o">)</span>
+<span class="m">6</span>
+&gt;&gt;&gt;<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>&lt;24174F3E-2670-79AC-4F26-F8B49774194A&gt;<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">&#39;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib&#39;</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">&#39;/opt/X11/lib/libcairo.2.dylib&#39;</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">&#39;/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib&#39;</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">&#39;/opt/X11/lib/libcairo.2.dylib&#39;</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">&#39;/usr/local/lib/libcairo.2.dylib&#39;</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">&#39;/usr/lib/libcairo.2.dylib&#39;</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>&gt;<span class="w"> </span>3Q47_recH.pdb
+$<span class="w"> </span>reduce<span class="w"> </span>3Q47_pep.pdb<span class="w"> </span>&gt;<span class="w"> </span>3Q47_pepH.pdb
+</code></pre>
+</div>
+
+<h3 id="preparing-receptor">Preparing Receptor</h3>
+
+<pre><code>$ 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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py&quot;</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">&#39;_adfrcc&#39;</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>&lt;424BF61E-BF0F-351E-B546-E82EBBD8FBF5&gt;<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">&#39;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib&#39;</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">&#39;/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib&#39;</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">&#39;/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib&#39;</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">&#39;/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib&#39;</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">&#39;/usr/local/lib/libgomp.1.dylib&#39;</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">&#39;/usr/lib/libgomp.1.dylib&#39;</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">&quot;Authorization: Bearer QQ==&quot;</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
new file mode 100644
index 0000000..4b1bad2
--- /dev/null
+++ b/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png
Binary files differ
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">
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+ <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" />
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+ <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>
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+
+<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">&quot;</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">&quot;</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">&quot;</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">&quot;</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>-&gt;<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">&#39;stable&#39;</span>
+<span class="o">==</span>&gt;<span class="w"> </span>Updating<span class="w"> </span>Homebrew...
+<span class="o">==</span>&gt;<span class="w"> </span>Installation<span class="w"> </span>successful!
+
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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">&#39;eval &quot;$(/usr/local/bin/brew shellenv)&quot;&#39;</span><span class="o">)</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>/Users/navanchauhan/.zprofile
+<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">&quot;</span><span class="k">$(</span>/usr/local/bin/brew<span class="w"> </span>shellenv<span class="k">)</span><span class="s2">&quot;</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>&gt;<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>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">m4</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">autoconf</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span>ca-certificates
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span>openssl@3
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span>pkg-config
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">readline</span>
+<span class="o">==</span>&gt;<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>&gt;<span class="w"> </span>Fetching<span class="w"> </span><span class="nv">pyenv</span>
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Pouring<span class="w"> </span>ca-certificates--2024-03-11.all.bottle.tar.gz
+<span class="o">==</span>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<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>&gt;<span class="w"> </span>Installing<span class="w"> </span><span class="nv">pyenv</span>
+<span class="o">==</span>&gt;<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>&gt;<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">&quot;~/Developer/scrippstuff&quot;</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...
+-&gt;<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">&#39;Mac/Tools/pythonw.c&#39;</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">&#39;Doc/library/ctypes.rst&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Lib/test/test_str.py&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Lib/test/test_unicode.py&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/_ctypes.c&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/callproc.c&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/ctypes.h&#39;</span>
+patching<span class="w"> </span>file<span class="w"> </span><span class="s1">&#39;Modules/_ctypes/callproc.c&#39;</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">&#39;Mac/Modules/qt/setup.py&#39;</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">&quot;help&quot;</span>,<span class="w"> </span><span class="s2">&quot;copyright&quot;</span>,<span class="w"> </span><span class="s2">&quot;credits&quot;</span><span class="w"> </span>or<span class="w"> </span><span class="s2">&quot;license&quot;</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>more<span class="w"> </span>information.
+&gt;&gt;&gt;<span class="w"> </span>from<span class="w"> </span>random<span class="w"> </span>import<span class="w"> </span>randint
+&gt;&gt;&gt;<span class="w"> </span>randint<span class="o">(</span><span class="m">0</span>,10<span class="o">)</span>
+<span class="m">6</span>
+&gt;&gt;&gt;<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>&lt;24174F3E-2670-79AC-4F26-F8B49774194A&gt;<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">&#39;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib&#39;</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">&#39;/opt/X11/lib/libcairo.2.dylib&#39;</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">&#39;/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib&#39;</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">&#39;/opt/X11/lib/libcairo.2.dylib&#39;</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">&#39;/usr/local/lib/libcairo.2.dylib&#39;</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">&#39;/usr/lib/libcairo.2.dylib&#39;</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>$<span class="w"> </span>reduce<span class="w"> </span>3Q47_rec.pdb<span class="w"> </span>&gt;<span class="w"> </span>3Q47_recH.pdb
+$<span class="w"> </span>reduce<span class="w"> </span>3Q47_pep.pdb<span class="w"> </span>&gt;<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py&quot;</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>&lt;module&gt;
+<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">&quot;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py&quot;</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">&#39;_adfrcc&#39;</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>&lt;424BF61E-BF0F-351E-B546-E82EBBD8FBF5&gt;<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">&#39;/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib&#39;</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">&#39;/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib&#39;</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">&#39;/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib&#39;</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">&#39;/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib&#39;</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">&#39;/usr/local/lib/libgomp.1.dylib&#39;</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">&#39;/usr/lib/libgomp.1.dylib&#39;</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">&quot;Authorization: Bearer QQ==&quot;</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>
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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>