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– AGMBuild is a tool to generate molecular models. It can output compatible with OpenMM 1.x and 2.x. – It generates new models/files for use in OpenMM 1.x and 2.x. – Upon starting the application, a dialog will prompt the user for the name of the model/files, and the charge definition. The user will also need to select file extension of the input/output files (for OpenMM 1.x), and the atom types to be used. All other settings can be left blank for this example. – It is designed as an easy to use and interactive molecular design tool, however, it is also possible to do a more traditional molecular modeling process using the application if the user wishes. – AGMBuild is free for non-commercial use, however, for commercial use, there are a number of extra options. – The source code for AGMBuild is available at [git.autodesk.com](git.autodesk.com) and is released under the BSD licence. 1) Installation and Using AGMBuild  =================================== AGMBuild is written in Python and uses PyQt5. – Python is an interpreted object-oriented programming language with an interactive shell. Python is a scripting language with a simple, straightforward syntax and semantics. – PyQt5 is a cross-platform GUI toolkit, allowing for development of applications on Unix, Mac, and Windows, without the need for additional ports. – The AGMBuild source code is written for all major operating systems, including Linux, Mac, and Windows. The installation of AGMBuild depends on the requirements of the user’s operating system. – For the Mac, the AGMBuild application can be downloaded from our GitHub repository, [ AGMBuild requires a license agreement before installation.  – For the Windows version of AGMBuild, the installation is a single executable file, and requires no other software.  – For the Linux version of AGMBuild, the application is also a single executable file, but requires a Debian



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AGM Build gives you an intuitive graphical interface for building aqueous models for molecular dynamics and free energy calculations of biomolecules such as proteins, nucleic acids, and their complexes. The input of your target system (such as a protein) is obtained directly from X-ray crystallography, NMR or molecular modeling software. For example, if your target is the protein troponin C, the residues of which are 1) protein crystal structure (PDB code: 4PLU), 2) NMR resonance assignment (PDB code: 2P23), or 3) modelled from a homologous structure (PDB code: 1CJW) then it will select from the respective options. The output of your model is saved in a.mx file that is used for all further processing. If applicable, an input PDB file and/or the identifier of the actual template PDB code (PDB token) are also generated. The following sections describe the various options of this tool.  Version 1.2.0 ![](./FIGURE1_AGM_Build_1.2.0.png)   Version 1.2.0  **Revision history**: In this release we have made the following changes and improvements: 1.  Added a new option under the “Molecular atom types” section to add PQR files as an alternative way of defining molecular atom types. The structure of a PQR file is explained in the help file.  2.  Added a new option under the “Molecular atom types” section to edit the default atom type for hydrogen atoms.  3.  Added an option under the “Options” section to create a new PQR file.  4.  Added an option under the “Options” section to change the geometry for the superimpose window.  5.  Added an option under the “Options” section to choose the type of hydrogen bonds.  6.  Added an option under the “Options” section to change the name of the output files (that are generated in.mx format).  Remarks: Currently this tool is not able to directly import the lab AMBER or Gaussian.amber format files that contain the atom types as described in the help file. However, once the needed atom types are added to the PQR 2f7fe94e24



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1.3 Simulation Results The simulation results tab is where the results of the simulations run using the AGM Build



What’s New In?


The program consists of several visual parts that are used to describe and control the output of the calculations. The visual parts include: • *Command Line Tool* The Command Line Tool is used to export selected models. Models can be exported to a text file or to a SciLab.slx or.slv file. • *Model Builder* The Model Builder is used for model preparation. Several models can be created on one script. Models can be created with the so called fragment assembly model or with a molfile. • *Model Producer* The Model Producer is used for calculating the atomic groups (AGs) for the AGM Build. The AGs of the model can be calculated with one of four different AG generation methods, plus one validation method. Once the group generation is complete the user can preview the AGs, and at the same time, can calculate the alignment matrix for every AG. • *Model Viewer* The Model Viewer is used for showing and editing the groups. The Model Viewer provides a graphical user interface for viewing and editing groups and graphs. Each graphical view of the group shows its information. The graphical views include: • ‘*Atoms and Bonds*’ that shows the group and its connectivity. • ‘*Capping groups*’ that shows the smallest set of atoms required to connect to the group. • ‘*Active*’ and ‘*Inactive*’ that shows in which mode the current group is. • ‘*Calculation*’ that displays all the values for atoms and bonds connected to a group. • ‘*Graphical*’ that shows in which way the group is represented. • ‘*Prototype*’ that shows the visual prototype of the group. • ‘*Members*’ that shows the distribution of atoms and bonds within the group. • ‘*Parts*’ that shows which atoms are the representative atoms for the group. • ‘*Possible*’ and ‘*Fixed*’ that show in which mode the current group can be used. • ‘*Propagation*’ that shows which atoms of the group are connected to which other groups. • ‘*Capped parts*’ that show the composition of the capped group. • ‘*Count*’ that shows the number of atoms of the group.


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System Requirements:


Minimum: OS: Windows XP SP3 or Windows 7 CPU: 1.4 GHz Memory: 512 MB Graphics: Microsoft DirectX 9.0 compliant video card with a minimum resolution of 1024×768 Network: Broadband Internet connection DirectX: Version 9.0 Hard Drive: 3.0 GB Additional Notes: All downloaded games and demos will be installed on the main hard drive (C:) Recommended: CPU: 2.0 GHz



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