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Parameterizing an Isopeptide Bond for Molecular Dynamics Simulation in AMBER

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I am frequently asked to set up and parameterize difficult systems for molecular dynamics simulation, and thought I would make it easier for others to do the same in the future by writing some tutorials.

Here, we will set up a diubiquitin system with a K11 isopeptide linkage joining two chains. The info here can be applied to any systems that have residues that join in ways different from the usual peptide sequence.

Here we will use the AMBER forcefield, parameters, and file types. You’ll learn about how AMBER defines new resides in perhaps more detail than is necessary. You should have basic experience preparing PDB structures for MD simulation (tutorials here) and have a general understanding of what atom types and forcefields are (helpful review article).

Preparing Membrane Protein Systems for AMBER Using Dabble

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Setting up membrane protein systems for molecular dynamics simulation can be a pain, especially when using membrane protein builders designed for other software packages.

I’m happy to announce the release of Dabble, a membrane protein builder and parameterizer that is designed to be forcefield agnostic. Currently it supports both AMBER and CHARMM parameter sets, and eliminates many problems with system setup, including issues with atom naming!

Dabble

Compiling VMD as a Python Module

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Visual Molecular Dynamics (VMD) has a very powerful built-in language for manipulating molecular structures in a variety of file formats with a powerful atom selection.

It can actually be built as a shared library that can be loaded into Python and used in your code, for all sorts of analysis scripts. However compiling it as such can be a bit tricky. This blog post will help you out.

If you are looking to compile regular VMD or want a better overview of the whole process, please reference this earlier post.

Compiling VMD With Python Support

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Visual Molecular Dynamics (VMD) is great. Tcl isn’t (IMO). Fortunately, VMD has support for a fully-featured Python interpreter! Unfortunately, this support isn’t built into the available binaries, and compiling it is kind of weird and confusing. Fortunately, I’ve done all the being confused for you and have written this guide on compiling VMD from source.

New Website

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After many years of ignoring my Wordpress blog, I have finally migrated it to my domain. This will probably mess up my accidental SEO (I had the #1 hit on Google for “repair ipod database linux”), but is much, much more maintainable and hopefully accessible too.

How to Repair an iPod Database in Linux

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iPods, especially iOS devices, have often been a pain to manage without iTunes. For the longest time I had all my music on my Windows partition, and the only reason I would ever boot Windows is because I got a new album that I wanted to sync. Thanks to a wonderful combination of software, I never need to leave my nice command line / superior in every way Linux interface.

Easy, Safe Backups With Rsync and ZFS

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If you’re anything like me, you worry about losing your data and want to backup, but you’re too lazy to wait for everything to copy to a portable hard drive/ten thousand CDs/Dropbox/whatever. As a result, you rarely, if ever, run backups, and when your hard drive finally dies or you break your system somehow, you’re left with very outdated backups that are impossible to put back on your computer or nothing at all.

This is especially true if you run a bleeding-edge system like Gentoo, do kernel hacking, or enjoy running alpha builds to get new features- you will inevitably run into something that will break your system, and then in trying to fix it things only get worse. Backups then become important in not only preserving your data, but also serve to save your system in a stable state so that it may be restored easily if something breaks. Simply just copying your files onto a flash drive isn’t going to cut it.

I’ve managed to find a system that works quite well for me, and has actually saved me quite a bit of time in the past. It uses an external hard drive, rsync, and the ZFS file system to do incremental backups that preserve everything from ownership to permissions to dynamic linking. First I’ll tell you why this system is awesome, and then how to set it up yourself.

Rebinding the CapsLock Key to a Terminal

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If you’re anything like me, the Caps Lock key annoys the heck out of you. You’re typing along, not looking at your keyboard, when all of a sudden everythinG LOOKS LIKE THIS. Nevertheless, the key is in a convenient location (as evidenced by its often accidental pressing). I’ve found it immensely convenient to bind the key instead to Yakuake, a wonderful Quake-style terminal emulator for KDE. Now, whenever I press the Caps Lock key, a terminal pops down from the top of the screen, and I can press once more to banish it. It’s extremely useful if you’re on a Linux system and want easy access to the command line.

What follows is how to set this up on your own machine.