From 20b1941b672cb133ff4ca4c5cb45ae70cdd8c5f7 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 1 Jun 2020 12:27:12 +0530 Subject: Publish deploy 2020-06-01 12:27 --- posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS/index.html | 4 ++-- posts/2020-05-31-compiling-open-babel-on-ios/index.html | 2 +- .../index.html | 8 ++++++++ posts/index.html | 2 +- 4 files changed, 12 insertions(+), 4 deletions(-) create mode 100644 posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html (limited to 'posts') diff --git a/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS/index.html b/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS/index.html index c9f79b4..9431830 100644 --- a/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS/index.html +++ b/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS/index.html @@ -1,4 +1,4 @@ -Fixing X11 Error on macOS Catalina for AmberTools 18/19 | Navan Chauhan
Navan Chauhan
2 minute readCreated on April 13, 2020Last modified on May 18, 2020

Fixing X11 Error on macOS Catalina for AmberTools 18/19

I was trying to install AmberTools on my macOS Catalina Installation. Running ./configure -macAccelerate clang gave me an error that it could not find X11 libraries, even though locate libXt showed that my installation was correct.

Error:

Could not find the X11 libraries; you may need to edit config.h
+Fixing X11 Error on macOS Catalina for AmberTools 18/19 | Navan Chauhan
Navan Chauhan
2 minute readCreated on April 13, 2020Last modified on June 1, 2020
Fixing X11 Error on macOS Catalina for AmberTools 18/19
I was trying to install AmberTools on my macOS Catalina Installation. Running ./configure -macAccelerate clang gave me an error that it could not find X11 libraries, even though locate libXt showed that my installation was correct.
Error:
Could not find the X11 libraries; you may need to edit config.h
    to set the XHOME and XLIBS variables.
 Error: The X11 libraries are not in the usual location !
        To search for them try the command: locate libXt
@@ -13,4 +13,4 @@ Error: The X11 libraries are not in the usual location !
        To build Amber without XLEaP, re-run configure with '-noX11:
             ./configure -noX11 --with-python /usr/local/bin/python3 -macAccelerate clang
 Configure failed due to the errors above!
-
I searcehd on Google for a solution on their, sadly there was not even a single thread which had a solution about this error.
The Fix
Simply reinstalling XQuartz using homebrew fixed the error brew cask reinstall xquartz
If you do not have xquartz installed, you need to run brew cask install xquartz
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+

I searcehd on Google for a solution on their, sadly there was not even a single thread which had a solution about this error.

The Fix

Simply reinstalling XQuartz using homebrew fixed the error brew cask reinstall xquartz

If you do not have xquartz installed, you need to run brew cask install xquartz

Tagged with:
\ No newline at end of file diff --git a/posts/2020-05-31-compiling-open-babel-on-ios/index.html b/posts/2020-05-31-compiling-open-babel-on-ios/index.html index 5ead530..0adbc68 100644 --- a/posts/2020-05-31-compiling-open-babel-on-ios/index.html +++ b/posts/2020-05-31-compiling-open-babel-on-ios/index.html @@ -40,4 +40,4 @@ make[1]: ** make: *** [Makefile:129: all] Error 2

Strange but it is alright, there is nothing that hasn't been answered on the internet.

I did a little digging around and could not find a solution 😔

As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.

Packaging as a deb

This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.

Moment of Truth

So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted.

Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool

I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.

Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird.

So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!

I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️

The Final Fix ( For Now )

export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
 export BABEL_LIBDIR="/usr/lib/openbabel/3.1.0"
-

This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.

Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.

Hopefully, I add some more screenshots to this post.

Edit 1: Added Screenshots, had to replicate the errors.

Tagged with:
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This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.

Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.

Hopefully, I add some more screenshots to this post.

Edit 1: Added Screenshots, had to replicate the errors.

Tagged with:
\ No newline at end of file diff --git a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html new file mode 100644 index 0000000..aa9ff67 --- /dev/null +++ b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html @@ -0,0 +1,8 @@ +Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan
Navan Chauhan
2 minute readCreated on June 1, 2020

Workflow for Lightning Fast Molecular Docking Part One

My Setup

  • macOS Catalina ( RIP 32bit app)
  • PyMOL
  • AutoDock Vina
  • Open Babel

One Command Docking

obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
+

To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.

Let me break down the commands

obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt
+

pbpaste and pbcopy are macOS commands for pasting and copying from and to the clipboard. Linux users may install the xclip and xsel packages from their respective package managers and then insert these aliases into their bash_profile, zshrc e.t.c

alias pbcopy='xclip -selection clipboard'
+alias pbpaste='xclip -selection clipboard -o'
+
$(pbpaste)
+

This is used in bash to evaluate the results of a command. In this scenario we are using it to get the contents of the clipboard.

The rest of the command is a normal Open Babel command to generate a 3D structure in PDBQT format and then save it as test.pdbqt

&&
+

This tells the termianl to only run the next part if the previous command runs succesfuly without any errors.

vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
+

This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 without needing to type them manually.

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Navan Chauhan

Posts

Tips, tricks and tutorials which I think might be useful.

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Navan Chauhan

Posts

Tips, tricks and tutorials which I think might be useful.

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