http://autodock.scripps.edu These are the search results for the query, showing results 1 to 15. http://autodock.scripps.edu/faqs-help/how-to/how-to-setup-adt-scripts Describes how to configure Python interpreter so that it can find packages from MGLTools. This How-to is intended for users who use pre-compiled Python interpreter that comes with MGLTools. No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2009-09-08T17:24:00Z How-to http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-docking-parameter-file-for-autodock4 This How-to addresses using the python script 'prepare_dpf4.py' to create a docking parameter file for AutoDock4. This docking parameter file specifies (NOTE: You must have installed MGLTools). No publisher rhuey Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2009-08-25T17:15:02Z How-to http://autodock.scripps.edu/faqs-help/how-to/launching-autodock-using-adt A troubleshooting guide on how to launch AutoGrid/AutoDock using AutoDockTools' GUI. No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2009-08-20T17:28:25Z How-to http://autodock.scripps.edu/faqs-help/faq/why-do-the-results-differ-when-multiple-dockings-are-done-with-the-same-input Multiple docking calculations are specified in a docking parameter file using one of the following keywords: 'ga_run', 'do_local_only' or 'runs' plus 'simanneal'. In general, the results will differ between dockings when using the same input. No publisher rhuey Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2009-07-06T18:18:54Z FAQ http://autodock.scripps.edu/faqs-help/faq/problem-with-libstdc-so-6-on-linux What to do if you are getting "libstdc++.so.6: cannot open shared object file: No such file or directory" error message. No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2009-06-17T17:24:02Z FAQ http://autodock.scripps.edu/faqs-help/faq/how-do-i-install-autodock-on-linux-and-mac-os-x I've downloaded the tar.gz file containing the AutoDock and AutoGrid executables. How do I install them? No publisher morris Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. AutoDock AutoGrid 2009-06-04T17:31:44Z FAQ http://autodock.scripps.edu/faqs-help/faq/installing-autodock-on-windows How do I install AutoDock, AutoGrid and ADT on Windows? No publisher morris Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. AutoDock AutoGrid 2009-06-04T17:30:58Z FAQ http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide AutoDock is an automated procedure for predicting the interaction of ligands with biomacromolecular targets. The motivation for this work arises from problems in the design of bioactive compounds, and in particular the field of computer-aided drug design. Progress in biomolecular x-ray crystallography continues to provide important protein and nucleic acid structures. These structures could be targets for bioactive agents in the control of animal and plant diseases, or simply key to the understanding of fundamental aspects of biology. The precise interaction of such agents or candidate molecules with their targets is important in the development process. Our goal has been to provide a computational tool to assist researchers in the determination of biomolecular complexes. In any docking scheme, two conflicting requirements must be balanced: the desire for a robust and accurate procedure, and the desire to keep the computational demands at a reasonable level. The ideal procedure would find the global minimum in the interaction energy between the substrate and the target protein, exploring all available degrees of freedom (DOF) for the system. However, it must also run on a laboratory workstation within an amount of time comparable to other compu- tations that a structural researcher may undertake, such as a crystallographic refinement. In order to meet these demands a number of docking techniques simplify the docking procedure. AutoDock combines two methods to achieve these goals: rapid grid-based energy evaluation and efficient search of torsional freedom. This guide includes information on the methods and files used by AutoDock and information on use of AutoDockTools to generate these files and to analyze results. No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2009-05-29T16:52:48Z Reference Manual http://autodock.scripps.edu/faqs-help/tutorial/autodock-vina-video-tutorial This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL No publisher trott Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. Molecular Docking AutoDock Vina ADT AutoDockTools Redocking 2009-02-20T00:19:04Z Tutorial http://autodock.scripps.edu/faqs-help/manual/autodock-vina-manual-page Includes a summary of usage, configuration file examples and discussion of some parameters No publisher trott Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. Molecular Docking AutoDock Vina ADT 2009-02-19T23:28:59Z Reference Manual http://autodock.scripps.edu/faqs-help/how-to/force-a-non-rotatable-bond-to-be-considered-rotatable-in-adt ADT discriminates between rotatable bonds and non-rotatable bonds during ligand preparation. If bonds are classified as rotatable when they should be non-rotatable, they can be made non-rotatable using the GUI. However, if a bond is classified as non-rotatable when it should be rotatable, making the change is more complicated. This how-to explains the necessary steps to be taken in ADT. No publisher rhuey Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. ADT input file ligand 2008-10-28T23:47:07Z How-to http://autodock.scripps.edu/faqs-help/how-to/fixing-all-energies-are-equal-in-population-re-initializing-message The dlg file continues to fill with this line. No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. 2008-10-23T20:52:46Z How-to http://autodock.scripps.edu/faqs-help/faq/cant-find-or-open-a-file How do I tell AutoGrid/AutoDock where input files are? No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. Applications 2008-10-20T17:21:19Z FAQ http://autodock.scripps.edu/faqs-help/how-to/positioning-the-ligand This explains how to move a ligand independently of the macromolecule using our GUI. No publisher sargis Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. ADT AutoDockTools 2008-10-08T23:29:08Z How-to http://autodock.scripps.edu/faqs-help/faq/how-many-dockings-and-energy-evaluations-should-i-use-for-each-compound How much computational time should be invested in each compound? No publisher morris Copyright (C) The Scripps Research Institute, 2007-2009. All Rights Reserved. AutoDock Virtual Screening 2008-03-07T03:58:50Z FAQ