It supports many of the most soughtafter features in a modern molecular dynamics program. Online help for glide is available in maestro, although the information in this manual is generally more comprehensive. Software available in the chemistry learning commons foster. Maestro is the portal to all of schrodingers computational technology far more than just a user interface, maestro also helps researchers organize and analyze data. Using the amber force field in desmond the desmond users manual has instructions on converting amber prmtop files to maestro desmond format. Dock and autodockvina are less user friendly, but also freely available. Ortec maestro32 mca emulator for microsoft windows 2000 professional and xp professional a65b32 software users manual software version 6. Maestro is the culmination of years of research and development. Schrodinger the minnesota supercomputing institute. Performing common tasks in maestro 11 building and modifying structures click to open the 3d builder palette. We replaced almost all of the images with maestro related images, but there were a very small number that are still smartsdr.
Introduction the glide user manual is intended to help you perform ligand database screening and highaccuracy docking with glide. Select edit adjust quick torsion from the top menu, then click on a bond to select it. Software available in the chemistry learning commons. Installing schrodinger suite columbia university libraries. Introduction desmond is a new explicitsolvent molecular dynamics program developed by d. In this document, to type text means to type the required text in the specified. Glide offers the full spectrum of speed and accuracy from highthroughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at every level. Revision history cecile lin this manual is written without any warranty. Structureae a eeg g e page 1 of 11 structurebased virtual screening using glide created with release 144 in this tutorial we will use glide to perform a virtual screen for potential inhibitors of factor xa. Maestro 11 beta reference guide this document provides an illustrated highlevel description of the new and significantly changed features available in the maestro 11 beta release. The 3d builder palette can be used to edit existing entries or create new structures in the workspace.
Desmond was created from scratch with an emphasis on accuracy, speed and scalability. The maestro11 beta can be enabled by choosing try maestro 11 from the welcome screen, or by selecting switch to maestro 11 from the maestro menu and restarting maestro. It is a visual intensive software and you are recommended to use. Schrodinger is a scientific leader in computational chemistry, providing software solutions and services for life sciences and materials research. Maestro adds uniformity across many product lines of schrodinger inc. The submission of a schrodinger job is different from any other job submission. Please see instructions to open schrodinger suite 20194 graphical user interfaces on macos 10. Significantly enhanced usability built on maestro s longstanding impressive visualization and analysis tools makes maestro 11 a versatile modeling environment for all researchers.
Mini maestro 12channel usb servo controller fully assembled labeled top view. For more details, please see how to run schrodinger software at stanford. Ligprep user manual data science and information technology. On this page you will find instructions for software download and installation, as well. Apr 12, 20 we will use both the ugly commandline approach and the graphical user interface maestro program throughout the docking procedure and we will see that there are advantages for both. Introduction to schrodingers software yuk sham feng chen center for drug design university of minnesota msi fall tutorial 2011 software usage outline. This tutorial is for a docking beginner and you can refer to the online user manuals if you are seeking more details or flexibility for any step.
Proceed to configuration below before running maestro for the first time. Glide is run primarily from the maestro graphical user interface, but can also be run from the command line. Lsoft sweden ab users manual listserv maestro, version 2. As a small addition to that, here are some notes on how to convert the jac benchmark.
The maestro user guide was written by taking a copy of the smartsdr user guide, tearing it down and building it back up for maestro. Macromodel are registered trademarks of schrodinger, llc. Dec 01, 2016 this feature is not available right now. View and download maestro 100 series user manual online. Schrodinger academy maestro 11 tutorials structurebased virtual screening using glide. Biologics, smallmolecule drug discovery, and materials science. Please note that schrodinger is only configured to submit jobs to mesabi, so you must be connected to mesabi if you would like to submit a job from the maestro interface. Schrodinger high performance computing cluster at cwru. Maestro comes with automatic contextsensitive help autohelp, balloon help tool tips, an online help facility, and a set of manuals.
How do i align two protein structures in maestro and manually change amino acid. View and download maestro a2200a user manual online. How can i extract top ligands with schrodinger maestro glide, after docking xp and. Schrodinger has developed a workaround, which requires launching guis from the commandline. The maestro is a microprocessorbased power and energy meter that uses the latest technology to. Quick install guides for release 20201 click icon to download. Figure 11 as the user builds the model through a combination of menu choices and keyboard entry the maestro continuously updates and displays a colorcoded picture of the model. In this manual it is assumed that you have followed the software setup instructions in the maestro installation guide and have successfully installed the software.
Glide structurebased virtual screening using glide 20163. See help manual index to access schrodinger s library of tutorials and technical. By working closely with our users, maestro was created to be the user environment that is both intuitive and allows our users to get work done efficiently. The primary goals of the research in the baker group over the past several years have been to predict the structures of naturally occurring biomolecules and interactions and to design new molecules with new and useful functions.
The molecules that contain the alternative cores must be prepared as allatom, 3d structures, and must be labeled with the attachment points. Page 1 maestro 100 series gsmgprs modems eco lite extended user manual rev. Macromodel quick start guide university of california. Glide user manual data science and information technology. The glide user manual is intended to help you perform ligand database screening and highaccuracy docking with glide. Introduction to obtain the full performance from the maestro, we recommend that you read this manual carefully. For information on using maestro, see the maestro online help or the maestro user manual. Maestro also contains many generalpurpose features which make it useful as a standalone product or in conjunction with third party software. Many of the applications also have commandline interfaces. Introduction ligprep is a robust collection of tools designed to prepare high quality, allatom 3d structures for large numbers of druglike molecules, starting with 2d or 3d structures in sd or maestro format. Jaguar is a highperformance ab initio package for both gas and solution phase simulations, with particular strength in treating metal containing systems, making it the most practical quantum mechanical tool for solving realworld problems. The maestro tracker component is the component that collects the tracking events that are. Schrodinger 101 sw main street, suite 0 portland, or 972043212. The software described in this manual is provided on the cd that accompanies the maestro or as a download from elmos web site.
Schrodinger s graphical front end is called maestro. Click and drag left or right to adjust the torsion. To help you quickly get acquainted with maestro, we have put together an eightpart series in which we demonstrate and. Maestro is the portal to all of schrodingers computational technology far more than just a user interface, maestro also helps researchers organize and analyze. You and your mouse left button click on atom to select atom. This manual contains an introduction to the maestro graphical user interface gui and a description. The maestro user interface component is the actual user interface for mail jobs, tracking data, and recipient lists. Bill jorgensen that performs monte carlo statistical mechanics simulations of ligands, peptides, proteins, and nucleic acids in the gas phase or in solution. Schrodinger s license is based on tokens which are reserved when you run jobs with multiple sub jobs. Macromodel quick start guide university of california, irvine. Composer user manual maestro software manual simpliq software manual simpliq command reference manual canopen implementation guide maestro setup maestro getting started drive setup drive installation system programming tuba cornet maes tro maestro installation guide maestro software manual figure 12.
Schrodinger has its own job control mechanism for submitting jobs which runs on top of the sun grid engine. The resulting structures can be saved in either sd or maestro format. Glide offers the full spectrum of speed and accuracy from highthroughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at. It is usually a good idea to change to the desired working directory before starting maestro. Home page documentation can be found in the help menu in maestro. Before starting maestro, you must set the schrodinger. This is the best place to read jaguar manual schrodinger before service or repair your product, and we hope it can be fixed perfectly. This manual contains an introduction to the maestro graphical user interface gui and a. Bioluminate, desmond, knime extensions, maestro, opls3, piper.
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