ADCP Suite and AGFRGUI in Ubuntu VM on Apple Silicon

Intro This post is a guide to setting up a virtual machine (VM) for various Linux x86_64 programs in the ADCP suite, now provided in a self-contained micromamba environment. Following the outlined instructions, a desktop will be installed for the VM. Graphical programs such as AGFRGUI can be used through the desktop. Furthermore, on Mac comput... Read more 17 Dec 2023 - 8 minute read

Peptide Docking and OpenMM Minimization with ADCPv1.1, Interfacing RDKit, and MM/GBSA Calculation in Amber

Intro This post is based on some basic knowledge and familarity with peptide docking using Autodock CrankPep (ADCP), as described in the previous post. The intent of the post is to introduce to our lab members the new features in ADCP v1.1, including the most useful OpenMM minimization and the incorporation of D-amino acids, followed by some a... Read more 08 Nov 2023 - 7 minute read

Peptide Docking with ADCPv1.0, Post-processing, and Induced-fit Optimization with Vina

Intro This post describes peptide docking using Autodock CrankPep (ADCP) (Version 1.0 rc1), some post-processing including converting the output structure of the docked peptide into a charged RDKit molecule, and finally a very primitive “induced-fit” refinement using the local optimization function, optimize, from AutoDock Vina’s Python binding... Read more 27 Oct 2023 - 16 minute read

ADFR Suite and ADT in Ubuntu VM on Apple Silicon

Intro This post is a guide to setting up a Linux virtual machine (VM) with a desktop on Mac computers with Apple Silicon (M1/M2), for the purpose of installing and running the x86_64 programs in the ADFR suite and AutoDockTools (ADT) on such devices. Apple Silicon uses the ARM64 architecture. Programs that were not built in this architecture c... Read more 16 Oct 2023 - 12 minute read

About the Author

Hello traveler! I’m @rwxayheee. I’m currently a chemistry graduate student at tOSU. I was born and raised in Hangzhou from the East China. My hobbies are fictions, travel, gaming, medicinal chemistry and coding. When I was a kid I used to love writing for fun, but never start a professional blog for myself (this really isn’t one either). I crea... Read more 15 Oct 2023 - less than 1 minute read

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