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Protocols for running DOCK software on AWS. Specifically DOCK 3.8 (and others in the DOCK3 family) ...software, the toolchain we use can be extended to facilitate setting up an AWS Batch environment for any sort of massively parallel computation.

* Tutorial 1: [[AWS:Set up account]] * Tutorial 2: [[AWS:Upload files for docking]]

[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locall

Current method to select tranches to dock in ZINC 22 . * AWS, .s3 suffix

= Introduction to the aws-setup platform = ...The power of these scripts lies in the deep knowledge they encapsulate of AWS systems.

* become s_jji on n-1-17 * edit as you see fit including new dock executable

...oposal for a job configuration file that can be used to manage LSD jobs in DOCK 3.8 preset: aws

DOCK 3.8 has been the primary version of DOCK 3 since January 2021. DOCK 3.8 is now organized into a number of smaller repositories, each with a spe

* Tutorial 1: [[AWS:Set up account]] * Tutorial 2: [[AWS:Upload files for docking]] THIS TUTORIAL

* Tutorial 1: [[AWS:Set up account]] * Tutorial 2: [[AWS:Upload files for docking]]

* Tutorial 1 AWS:Set up account THIS TUTORIAL * Tutorial 2: [[AWS:Upload files for docking]]

[[Category: AWS DOCK]] ...r MAX_CPUS values (for example, after getting a limit increase approved by AWS support). Just provide the same parameters as before (name, region, etc) ex

...nformation on how to set up spot fleet permissions, see here: https://docs.aws.amazon.com/batch/latest/userguide/spot_fleet_IAM_role.html#spot-fleet-roles description: Should be either a directory or file hosted on s3

* Tutorial 1: [[AWS:Set up account]] * Tutorial 2: [[AWS:Upload files for docking]]

This document describes where files live, officially, on the cluster. Also mirrored on AWS.

...rmal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite * this can all be done on gimel2

...-started/. You can install docker desktop to your personal machine, or log on to a machine where docker is already installed. On a linux/mac/windows computer with docker or docker desktop installed, run t

The History of [[DOCK]], longish version ...ation has been found, it is evaluated by any of several scoring functions. DOCK may be used to explore the binding modes of an individual molecule, or be u

...rt/lsregister -kill -r -domain local -domain system -domain user ; killall Dock To pause, run the following query on the slave server:

How to dock in DOCK 3.8.0 Related page: Docking Analysis with DOCK 3.8