MacroModel® Interactive Molecular Modeling System Version 7.0
MacroModel User Manual
© 1999 Schrödinger, Inc. All rights reserved.
Derived from material which is © Columbia University
Table of Contents
User Manual Table of Contents
CHAPTER 1 MacroModel Overview 9 1.1 Conventions Used in This Manual 9 1.2 New Features 11 1.3 General Information 13
CHAPTER 2 Input Mode and General Operation 15 2.1 MacroModel Windows 15 Message Window 16 Main Structure Window 17 Main Button Panel 18 Mode Options Window 18 Submode Options Window 19 Control Window 20 Popup Prompt 20 Help and Documentation 20 Structure Input 22 Atom Picking 22 SYSTEM 23 OSF/Motif Window Manager 23 Structure File Reading and Writing 24 File Reading 25 File Writing 27 Foreign Structure Files 28 Compressed MacroModel Files 29 2.2 MacroModel 2D: X-Windows (Two-Dimensional) Operation 29 Global XY Translations 30 Global XY Rotations 30 Scaling and XY Clipping 31 X Emulators 31 2.3 MacroModel 3D: GL (Three-Dimensional) Operation 32 Scaling and XY Clipping 32 Operation of the 3-Button Mouse 32 Global Transformations 33 Global Rotation - Rot X, Rot Y, Rot Z Buttons 34 Global Centering and Translation - Right Mouse Button. 35
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Zooming, Clipping Planes and Depth Cueing - Control Window. 36 Torsion Angle Rotations 37 Specific Torsion Angle Setting - ROTAT Button 38 Real Time Torsional Rotations - Rot T Button 38 Molecular Translations and Rotations (Docking) 40 Incremental Translations and Rotations - Orient Sub- mode 41 Real Time Molecular Translations and Rotations - TR- Mol Button 42 Monitoring Geometrical Changes 43 Monitoring Specific Distances and Angles - ADist, BAngl and DAngl Buttons 43 Bump Checking - Opt Button 44 Structural Rendering Options 45 Wire Frame Line Diagrams 45 Polytube Diagrams - Polytube Button 46 Ball-and-Stick and CPK Space-filling Diagrams - Ball-and-Stick and CPK Buttons 46 Stereo - Stereo button 47 Hardware Stereo 47 Setting MacroModel Colors - Set Colors 48 Resizing of CPK spheres - CPK Resize 48 2.4 Structure Building 49 Modifying Existing Structures 50 Structure Files from External Sources 51 Manual Molecular Construction 52 Conformationally Flexible Molecules 53 Molecular Complex Construction and Docking 53 Renaming Facility - Renam 54 Extended Atom Types 56
CHAPTER 3 Energy Mode and Operation with BatchMin 57 3.1 MacroModel Force Fields 57 Differences in force field equations 58 Differences in parameters 59 3.2 Solvation Treatment 61 3.3 Convergence 62 Running Energy Calculations with MacroModel/ BatchMin 62
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3.4 Setting Up BatchMin Energetic Jobs 63 Running Old Command Files 63 Examining BatchMin COM Files 64 Multiple BatchMin Operations - NxtOp Button 64 3.5 Starting BatchMin Energetic Jobs 65 3.6 Monitoring BatchMin Energetic Tasks 68 3.7 Terminating BatchMin Energetic Tasks 69 3.8 Halting BatchMin Tasks 69 3.9 Putting BatchMin Tasks to Sleep 69 3.10 BatchMin Communication File Disposition 70 3.11 Typical BatchMin Energetic Tasks 70 Energy or Gradient Calculation 71 Button Description of operation 71 Full Structure Energy Minimization 71 Button Description of operation 71 Substructure Energy Minimization 73 Button Description of operation 73 Molecular, Stochastic Dynamics And Mixed Mode 75 Conformational Searching - Monte Carlo Method (MCMM) 77 3.12 FFVIEW: Force-field parameter viewer/editor 79 Interaction display panels 80 Viewing the force-field 82 Editing the force-field 82
CHAPTER 4 Analyze Mode 85 4.1 Internal Coordinate Monitors - ADist, BAngl, DAngl 86 4.2 Atom Numbers - FAtm, NAtm, FRes, NRes, Num, Clear 86 4.3 Textual Captions - AddLb 87 4.4 Averaged Atom Positions or Centroids - AveAt 87 4.5 Multiple Conformation Filtering - Filtr 88 4.6 Multiple Substrate Docking via a Dock File - DFile 90 4.7 Dot Surfaces - SURFAC submode 90 4.8 Contour Panel (Ramachandran Plots) - Cntr 91 4.9 Plotting of torsion angle - energy profiles - Plot1D 94 Main Controls 94 Interacting with the plot 97 Changing the Plot Appearance 98 4.10 Structure Plotting - Plot 98 Wireframe 99
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PixelMap 99 Other 100 4.11 Boolean Operations on Atom Sets - ABool 101 4.12 Volume Boolean Operations On Molecules - MBool 102 4.13 Ribbn (Ribbon Panel) 103 4.14 Movie 105 4.15 Hydrogen Bonding (Hbond, HPref Buttons) 105 4.16 Photo Mode 106 4.17 ASL (Atom Specification Language) Panel 106 The Buttons 106 Commands (classes) and Properties 106 Operators 107 Operator Priority (decreasing priority) 107 Full Descriptions of Commands 108 Abbreviations/Aliases 109 Some Examples 109 Notes 110
CHAPTER 5 Other Programs 111 5.1 Xrbm 111 Overview 111 Running xrbm 111 Monitoring a BatchMin job 112 Button Descriptions 112 Troubleshooting 113
Appendix 1 Installing MacroModel 115 MacroModel Directory Structure 115 Environment Variables 115 INClude directory paths 116 Silicon Graphics Installation 116 IBM RS/6000 Installation 118
Appendix 2 MacroModel on a Macintosh or PC 121 Macintosh 121 Using MacX 122 PC 124
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Appendix 3 Setting Up MacroModel and BatchMin Communica- tion 125 Summary 125 How To Install Entries In hostfiles.dat 126 Adding Entries For Locally Executing Jobs 126 Troubleshooting 127 Symptoms 127 Actions 128 NFS Style Remote BatchMin Installation Instructions 128 How the NFS Style Remote BatchMin Facility Works 128 How to install entries in hostfiles.dat 128 Establishing a shared directory with NFS 129 Notes 133 BatchMin Network Server Installation Instructions 134 Overview 134 Installation 135 Conventions 135 Step1: Informing inetd 136 Step 2: Get rsh running 139 Step 3: Try Out rbm and ’jump start’ the daemon 139 Step 4 (Optional): MacroModel -- Accessing the Serv- er From the Graphical User Interface 140 Some Final Notes 141 Trouble Shooting 141 Using the RPC Network Connection to Run BatchMin Manually 143 Installing Additional BatchMin Network Server Services 144 BatchMin Force Field, Solvent and atom.typ Files 145 Configuring bminrd, the BatchMin Network Server, to Start Automat- ically at Boot Time on an SGI 146
Appendix 4 MacroModel Atom and Bond Types 147 BONDS 147 ATOMS 148
Appendix 5 MacroModel Structure File Format 153 MacroModel Uncompressed File Format 154 Entry Header Line (first line of file or entry) 154 Atom Entries 154 MacroModel Atom Color Table 155 MacroModel/PDB Residue Types 156
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MacroModel Compressed Entry Format 157 Entry Header Line (first line of file or entry) 158 Atom Entries 158
User Manual Index 159
8 MacroModel User Manual Version 7.0 CHAPTER 1 MacroModel Overview
MacroModel V7.0 is the 1999 UNIX, X-Windows and GL release of Macro- Model. At this time, V7.0 will run with real-time, three-dimensional (3D) graph- ics on Silicon Graphics workstations (IRIX 6.5.2 or later operating system required), and on IBM RS/6000 workstations having Z-buffering, 24-bit IBM GL (not OpenGL) graphics, and the AIX 4.3.2.0 or later operating system. It will also run with small molecule real-time rotation (two-dimensional, i.e. 2D operation) using X-windows displays on a range of X-terminals including X-Terminals, X Windows-only workstations, and Macintosh and PCs running X Server emulators.
1.1 Conventions Used in This Manual
This manual uses the following conventions:
• courier font identifies program output listings. • bold courier font identifies items the user should type in verbatim. It is also used to denote file names, e.g. mystructure.dat. • italic courier font identifies things the user should replace when typing e.g. % ls filename • HELVETICA font indicates the names of MacroModel Motif Panels and Titles of Sections in the panels. • HELVETICA BOLD font indicates the names of MacroModel menu buttons and push buttons.
MacroModel User Manual Version 7.0 9 CHAPTER 1: MacroModel Overview
•
N.B. If you are viewing this document using HTML, the fonts will probably not appear as Courier or Helvetica; either way, however, they will appear as they do in the preceding paragraph.
• <> indicates something that should be replaced, e.g. ls <filename>. • [] indicates something that is optional. That is, it one may choose to include or not include the item, e.g. ls [-l].
• This icon indicates instructions which will result in an error if not followed correctly.
• This icon identifies items of special interest for novice users.
New • This icon is used to indicate a feature which is new in the current version of MacroModel.
• This icon is used to indicate a feature only available in the 3D version of 33DD MacroModel
• This icon is used to indicate a feature only available in the 2D version of 2D MacroModel
10 MacroModel User Manual Version 7.0 References to some environment variables are made throughout this manual. The environment variables and their default location are as follows:
VARIABLE VALUE MMOD_ROOT Directory where MacroModel was loaded from tape (e.g. /usr/people/mmod) MMSITEDIR $MMOD_ROOT/run/mmdat
MMEXECDIR $MMOD_ROOT/run/exec Table 1. MacroModel Environment Variables
When one of these variables appears in the text it is used to represent the value that is assigned to it (typically a directory path).
1.2 New Features
MacroModel V7.0 has a few enhanced capabilities relative to V6.5 , however our recent efforts on the graphical user interface side of MacroModel have been con- centrated on the development of Maestro. The major enhancements on the front- end of MacroModel 7.0 are bug fixes, as well as features that allow access to some of the new BatchMin methods. Below are a few of the enhancements for MacroModel:
• OPLS-AA force-field now available
MacroModel User Manual Version 7.0 11 CHAPTER 1: MacroModel Overview
• Atom replacement changed to not alter PDB residue, PDB atom name, MacroModel residue name when changing an atom type doesn’t change the element type. For example, when changing an O- to an O the PDB residue name, PDB atom name, and MacroModel residue name are left unaltered. • Now SimuT always sets arg 7 of MCSD command to be same as arg 7 of MDYN command (i.e. simulation temperature is always the same). In practice, argument 7 of the MDYN command is the value which is always used. • Atom Retyping has been altered. Now when one changes an atom type via the buttons in the BUILD panels the program checks to see if the change results in a different element type. If so, the atom and residue information is then altered to be UNKNOWN. Otherwise, if they are the same, the PDB atom name, PDB residue name and MacroModel residue type are left unaltered. Previously any change to the MacroModel atom type would result in this information being "lost" (i.e. changed to UNK). • Three new mmodsite.dat options: RESCALE_ON_READ, THICK_BONDS, LINE_SMOOTH.
If RESCALE_ON_READ is set to ON, then upon reading structure(s) from the READ panel a rescale is performed. Otherwise, use OFF to prevent automatic rescaling.
If THICK_BONDS is set to ON, the program starts with ThickBonds on. If OFF, the program starts with ThickBonds off. When Thick bonds is enabled in Macro- Model wireframe lines are drawn more than one pixel wide.
Setting LINE_SMOOTH is a hint. If set to ON and the system supports line smoothing, then line smoothing will be turned on by default. If OFF and the syt- sem suuports line smoothing, line smoothing will be turned off by default.
• NOTE: As of version 6.5 one can set the Cmpre (comparison atoms) for a conformational search via atoms in the working set. To do this place atoms in the working set. Then in CSRCH once MCrlo has been enabled select the Cmpre button. This will display a menu with a number of choices which include:
Working Set Atoms (Heavy Only)
12 MacroModel User Manual Version 7.0 Working Set Atoms (Heavy + H(O,S))
Choosing one of these will take the appropriate action using the working set atoms as the set of atoms from which to choose.
Installation of MacroModel workstations is outlined in “Installing MacroModel” on page 115 of this manual.
1.3 General Information
In MacroModel all energetic tasks are handled as separate processes operating with the BatchMin non-interactive modeling program. These processes may run on the local computer or on certain remote UNIX computers having NFS or TCP/ IP network connections to the graphics workstation. Multiple BatchMin tasks may run simultaneously and be monitored interactively by MacroModel. The sep- aration of interactive graphical tasks and non-interactive energetic tasks enhances productivity by allowing the user to switch easily between various interactive modeling tasks and cpu-intensive energetic calculations.
In 3D mode on the Silicon Graphics or IBM RS/6000 workstations, all operations are handled by simple 3-button mouse manipulations and allow rapid switching between global transformations (rotations/translations), torsional rotations and molecular transformations. Additionally, real time interactive distance/angle monitoring is provided along with display of molecular collisions (bump check- ing). Available structural representations include realistically lit polytube, ball- and-stick and CPK-like renderings in addition to simple line diagrams (wire- frame with bond orders coded by line width). All display windows may be moved and resized as desired using your workstation's window manager. Extensive use is made of Motif widgets including standard Mac-like file selectors and pop-up menus.
As in the previous release, we use the keyboard to modify the function of the mouse buttons. The keyboard commands require that the user learn the function of six specific keyboard keys; however, this method makes program operation much snappier, especially during bimolecular docking and other real time trans- formations. These keyboard commands are described in section 2.2 on page 29 and section 2.3 on page 32. of this document and summarized on the back of this manual.
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2D modeling can be carried out on X-11 terminals or terminal emulators and allows effective small molecule modeling. Since all menuing is handled using OSF/Motif and X-windows standards, program operation is the same in both 2D and 3D modes of operation. With X-terminal displays and small molecules, real time rotation is provided via the mouse as in 3D operation of the program. Thus, with the exception of real time translational and rotational substructure manipula- tions, space filling molecular representations, (and the 3D Control Window and VOLUM mode), the 2D and 3D versions operate identically. Stereo operation is provided via display of stereo pair images or utilizing hardware stereo (Crystal- Eyes) on Silicon Graphics workstations while in 3D mode.
Details of mouse-button operation are found in the file $MMSITEDIR/mmt- plx.doc and are available on-line (see below). The file can be printed for refer- ence because it describes how each button in the program operates. The term pick means to place the cursor over the desired item (an atom, a menu button or a selection from a popup menu) on the screen and select it using a mouse button.
14 MacroModel User Manual Version 7.0 CHAPTER 2 Input Mode and General Operation
2.1 MacroModel Windows
This release supports two display types: X-terminals for 2 1/2D modeling; and Silicon Graphics and IBM RS/6000 workstations for 3D modeling. User interac- tion with MacroModel is handled primarily by a mouse which is used to select buttons or atoms. Whenever keyboard input is necessary, popup windows appear which prompt for additional information. The cursor will move automatically into the popup window’s text input area. The user may select the default by either sim- ply pressing the left mouse button (without moving the mouse) or by selecting the OK button. Alternatively, the user may enter text into the popup prompt.
Textual program output is listed to a scrollable Message Window at the upper right corner of the screen. The main structure window (called MacroModel 3D GLX) is used for molecule display and graphical atom picking, and the vertical windows at the right side of the screen house the button menus. A small Control Window exists when running in the 3D (GL) mode of MacroModel and is used for Z-view clipping and for zooming. The default screen layout is shown below, but may be changed and saved to suit the user's preferences. All windows are under control of the workstation window manager and may be resized, reposi- tioned, iconified or enlarged to fill the entire screen.
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Default Screen Layout for MacroModel 3D GL Mode Shown (2D mode lacks Control Window)
MacroModel 3D GLX Message Window
Submode Options Main Structure Window Window
Mode Control Options Window Window
Message Window
The upper right-hand corner of the screen is occupied by a rectangular window where textual messages from the program are displayed. Instructions to the user are displayed in this window as is various output from MacroModel or BatchMin calculations. The Message Window actually consists of two subwindows with scroll-bars. The lower (gray) subwindow is where program output and messages appear. The upper (green) subwindow is a note-pad where information may be typed by the user or copied from the lower window by a standard Motif copy-and- paste operation using the mouse. The relative size of the two subwindows may be varied by moving the small square icon in the space between them with the left mouse button. To type memos into the note-pad, move the cursor into the green note-pad area and type the desired information. To copy from the program output window to the note-pad, select information in that window by holding down the left mouse button (the text selected will be highlighted), then move the cursor into the note-pad window and depress the middle mouse button.
16 MacroModel User Manual Version 7.0 Main Structure Window
Like all other MacroModel windows, the Message Window may be enlarged to fill the full screen by selecting the square maximize icon in the upper right corner of the window border with the left mouse button. Reselecting this icon returns the Message Window to its original size. The window may also be moved or other- wise manipulated using standard OSF/Motif window manager commands (see Window Manager description below).
The window menu icon brings up the Mofit window manager menu The maximize icon enlarges the message window Message Window
The minimize icon iconifies the message window This area is a user note-pad
This icon can be moved with the left mouse button to vary area sizes This area is for program output
Scroll bars for moving text inside windows
Information outside the viewing area of the subwindow can be accessed via the scroll bars below and to the right of each subwindow. Select the scroll bar icons with the left mouse button. Touching the arrow icons moves up/down one line at a time or right/left one character at a time. The scroll bars themselves are operated by positioning the cursor directly over them and depressing the left mouse button.
Main Structure Window
The large main window (title MacroModel 3D GLX when in 3D mode or Macro- model 2D when in 2D X-Windows mode) is used for display of chemical struc- tures. Various molecular structure rendering options (e.g. depth cueing, stereo, CPK, polytube) are available via the Opt button in upper right corner of the but- ton menu. The square icon at the upper right corner of the window border enlarges the main structure window to fill the full screen for photography. (Note when in 3D mode you may expand the window and get rid of all borders com- pletely by hitting the F1 function key which toggles into and out of photo mode.)
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You may have to move the Message Window down or to the left to see the max- imize icon. Reselecting the icon returns the window to its original size. Global, dual-axis structural rotations are carried out by holding down the middle mouse button and moving the mouse up/down (for x-axis rotation) or sideways (for y- axis rotation). Single axis rotation may be easier to control and is selected by picking RotX, RotY or RotZ. Pick any of these buttons twice to resume dual- axis rotation. Use a similar double pick of the Scale button as a general reset to rescale and recenter structures if they become too large, small, off center, etc.
Main Button Panel
Mode Options Window
The Mode Options Window is located in the lower portion of the Main Button Panel. It contains the three sections closest to the bottom of the panel. The bot- tom section controls file reading and writing (see below), undo and structure hold- ing; the middle section allows the selection of one of the three modes; and the third section allows the selection of any of the up to nine submodes. The default mode upon program startup is INPUT Mode. INPUT Mode is used for molecular structure building and geometrical manipulations. Other modes include ENRGY (Energy mode is for various BatchMin energetic calculations) and ANLYZ (Ana- lyze is for interrogating structures and modifying their display).
18 MacroModel User Manual Version 7.0 Main Button Panel
Submode Options Window
The Submode Options are located in the upper portion of the Main Button Panel. This is the second section (first gray section) from the top and includes buttons specific to the chosen submode. The default submode upon program start-up is ORGANI (Organic) and is used for constructing nonbiopolymeric organic mole- cules. Structures move from submode to submode, so structures that are built in a biopolymer submode (e.g. Peptide submode) can be modified in ORGANI sub- mode.
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Control Window
The Control Window is available only in the 3D (real time three-dimensional GL) mode of MacroModel. It is used to control zooming and z-clipping of com- plex structures. While the Control Window is normally displayed on the screen, it may be removed via a button in the Opt panel (the Opt panel is activated by selecting the Opt button located in the top right of the Main Button Panel. The lines and small buttons in the Control Window may be picked and manipulated with the middle mouse button. Operation of the Control Window is described in section 2.3 on page 32. The Control Window also contains the buttons used to perform substructure manipulation (RotT, TRMol, TRAll).
Popup Prompt
When some MacroModel buttons are picked, additional information is needed and the program prompts the user to obtain it. Such prompts are generally answered by selecting the desired item from a popup menu or by typing in a response on the keyboard followed by a
Help and Documentation
On-line help is available via a special green popup window (see below) which appears whenever the user picks the menu button of interest with the right-hand mouse button or picks the Help button from the top of the Main Button Panel. The Help Panel can be used to search the help database (i.e. the file mmt- plx.doc) for information on specific topics. These searches can be specified with user-selectable criteria and are not limited to help on Main Button Panel buttons. For example, to find out how to do 3D molecular translations in Macro- Model one could search the help file database by entering "Molecular Translations". This would then load the appropriate help into the Help Panel for the user to peruse. If the text is located in more than one help topic a list of the topic headings is displayed for the user to select from.
20 MacroModel User Manual Version 7.0 Help and Documentation
In addition to searching the entire help database one may also search the on- screen text. That is, the search will be limited to the help topic which is currently displayed. This is useful for help topics which have many lines of text. All searches can be carried out in a case sensitive or case insensitive manner.
MacroModel Help
DRAW (Manual drawing mode) A INPUT --> ALL --> DRAW B
Chains of bonded atoms (default carbon) are created by touching the screen inside the drawing box. Pointing to an existing atom* allows the addition of new atoms bound to the C existing atom. The default bond order is 1, but multiple bonds may be created by overdrawing existing bonds. Bond orders may be reduced by indicating the bond center after activating the DELET command. DRAW operates in a continuous chain (or ring if an old atom
Search On-screen Text: Find Next Find Prev D
Search Help File For: Search & Show Search Title E
Case Sensitive List All Help Quit F
The Help Panel contains the following sections:
A This line contains the Topic with an extended description in parentheses. In the diagram above the help for the DRAW button is displayed. B If the topic corresponds to a Main Button Panel button, this gives the path (sequence of button clicks) to activate that but- ton. C Scrollable help text section. D This row contains a text field and buttons which allow search- ing of the on-screen text. On-screen text searching is useful for locating particular information when there are many lines of help text displayed. E This row contains a text field and buttons which allow search- ing of the help database. Note that searching can be con- strained to search by title only. By default the whole help
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database is searched (Search Title is OFF). F Case sensitive searching can be toggled ON/OFF; List All lists all of the help topics in the database; Help provides help on the Help Panel; and Quit exits the Help Panel.
Structure Input
Structure input and molecule assembly with MacroModel V7.0 follows the same procedures used with previous versions of MacroModel. Thus, structures can be drawn freehand, assembled from fragments or built by modifying existing struc- tures. Drawing uses the Draw button and operates in continuous bond formation mode with all new atoms initially being defined as carbon. Drawing uses the left mouse button. To restart drawing a new chain, reselect the last atom picked to 'put the pen down', and then pick the new drawing origin (an existing atom or a blank place on the screen) and continue drawing. If a mistake is made in structure building, the Undo button can be used to retrieve the most recent previous struc- ture. Otherwise, use the DELET (delete) button to remove undesired structural fragments.
Atom Picking
So that desired atoms may be picked accurately in cluttered, complex structures, atom picking must be done with care. The graphical cursor is a small box which delineates the atom-picking area. An atom which is within that box will be picked if the left mouse button is depressed. It is important to position the cursor box so that ONLY the desired atom is within the box. For atoms with character strings which define the atom type (e.g. 'Br'), pick the lower left corner of the first charac- ter. A successfully picked atom will cause the picking box to flash and the termi- nal bell to ring. This is the default behavior and is called an audible bell. If the bell sound is turned off (via $MMSITEDIR/mmodsite.dat) then it is called a visual bell. The choice of audible or visual bell is made in the MacroModel site file. If an atom is missed, then reposition the cursor more carefully over the desired atom and depress the left mouse button again. Enlarging the structure (using Scale or the 3D Control Window) will help in cluttered environments.
22 MacroModel User Manual Version 7.0 SYSTEM
SYSTEM
This button replaces the TTY button which existed in Version 4.5 and earlier. SYSTEM brings up a list selector for choosing programs to run. By default the list includes a TTY (i.e. an xterm window), and xcluster. It may have additional default items depending upon on the platform you are running. The list may be added to or changed by editing the $MMOD_ROOT/run/mmdat/system.dat file. Also, any system.dat file in the local directory will override the one in $MMOD_ROOT/run/mmdat. Thus, one can set up a personal set of entries to use while leaving the default file alone (and not affect other users of Macro- Model).
Entries consist of one line separated by a colon. So, for example, the xterm choice is defined as:
TTY: /usr/bin/X11/xterm -sb
This will display the word 'TTY' in the list selector and execute the text to the right of the colon. In this case the command' /usr/bin/X11/xterm -sb is executed which will create an xterm with scroll bars (due to the -sb option).
When creating a TTY on some Silicon Graphics workstations you need to position the window by moving the outline with the mouse. Then press the left mouse but- ton to fix the position. Move the cursor into the new window whenever you wish to interact with it. Use the left Window Menu Icon on the Title Bar to remove the new window when you are done, type exit in the window to delete the window, or iconify the window with the Title Bar minimize icon (see below) to temporarliy store the window. Text windows or their icons will remain on the screen even after MacroModel is stopped.
OSF/Motif Window Manager
While any window manager can be used with MacroModel, it is assumed that the OSF/Motif window manager will be operating. In the diagram below are shown some of the major OSF/Motif window manager controls. One of the most useful controls is the Maximize Icon which causes the selected window to be expanded
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to fill the entire screen. Such enlargements are useful for photography of struc- tures, for studying program output in the Message Window and for reading lengthy on-line Help information. See your system documentation for operating details and any machine-specific functions of your window manager.
OSF/Motif Window Manager Controls Window Menu allows window moving Minimize Icon iconifies window resizing, raising, lowering, etc.
Title Bar Maximize Icon enlarges window to full screen size. Reselecting returns window to original size.
Resize Handles allow moving the window (middle mouse button) or resizing the window (left mouse button).
If windows are moved or resized during a modeling session, the new window lay- out will be lost when the program is stopped unless LayoutSave is activated via the Opt button.
Structure File Reading and Writing
MacroModel reads and writes molecular structure files via the READ and WRITE buttons in the lower mode options window. When either of these buttons is selected, a READ or WRITE panel pops up which is used to control file reading or writing. These panels remain displayed after a read or write operation is com- pleted and may be moved to convenient locations on the screen using the window manager (see Window Manager section above). These panels provide access to a Macintosh-like OSF/Motif File Selector via the OPEN button. They may be removed from the display by picking the QUIT button.
24 MacroModel User Manual Version 7.0 Structure File Reading and Writing
File Reading
If the READ button is selected, a Read file control panel (shown below) will appear on the screen. To select a file, either type the full name of the file (in your current directory) into the text window at the top of the panel or select Open to bring up the Mac-like OSF/Motif File Selector. The cursor must be in the area where the filename is to appear for typing to be accepted. If the file is specified by typing the name into the Read panel, then it may be read into MacroModel by picking the Read button at the bottom of the Read panel with the left mouse but- ton. If a file has more than one structure, they may be read sequentially by succes- sively picking the Read button. In the 3D version the name of the file will be displayed at the bottom of the main structure window.
File Reading Control Panel File name to be read. Position the cursor in this window and type the file name, or select the Open Button for the Motif file selector.
Read Scroll bars for viewing long file names
Number of next structure in file to be read
Number of structures to be read each time Start 1 Delete deletes the old structure before the new one is read, turn off if both structures to be kept. Total 1 Tile spreads out multiple structures on the screen, Delete Tile turn off if multiple structures should be stacked. Keep Current Set Keep Current Set prevents zeroing the working set. MModel P D B MModel and P D B are the two supported file formats. Read Open Quit READ - causes the selected structure file to be read. OPEN - accesses the OSF/Motif file selection widget. QUIT - removes control panel.
Default operation is that newly read structures replace old structures in the Main Structure Window (also called MacroModel 3D GLX window or Macro- Model 2D window). If you wish to read multiple structures onto the screen, select Delete to turn structure deleting off. Two file formats are available - Mac- roModel (MModel) or Brookhaven Protein Data Bank (PDB). We suggest keep- ing all files in MModel format because such structures are saved with high
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coordinate precision, full connectivity with bond orders, and atomic charges. PDB is primarily for reading Brookhaven files and requires either standard residue structures or connectivity records. If a PDB file is read, then bond orders should be checked, especially in nonstandard residue structures.
A Mac-like file selector (shown below) will appear on the screen if Open is selected. The files shown by default will be those having a .dat or .out suffix in the user's current working directory. If another suffix is desired, it can be spec- ified in the Filter field. The * character is used as a wild card for file name speci- fication. This panel is a standard OSF/Motif File Selector Widget and detailed instructions for its operation can be found in standard Motif manuals.
Type in file name (* for wildcard) in the OSF/Motif File Selector Filter window, then press the Filter button
Filter
Directories Files
.dat data files themselves File directories are listed here. Select by a double click with are listed left mouse button or click once here. Double click then select the Filter button. to select and Read.
Selection
Open Read Filter Cancel Open Only
Open file in Load the Files Open file in Selection Quit out of window with the the Motif Selection window and files matching the File Selector window but read the information in the do not read structure. Filter window. structure.
26 MacroModel User Manual Version 7.0 Structure File Reading and Writing
On most machines, files are most simply selected by double clicking using the left mouse button with the cursor positioned over the desired entry in the Files win- dow. If another directory is desired, double click the desired entry in the Directo- ries window. Alternatively, select a directory with the mouse from the Directories window and then select the Filter button, or select a file with the mouse from the Files window and press Open Read. Once a file has been read, the file selector will disappear.
File Writing
If the WRITE button is selected, a Write file control panel (shown below) will appear on the screen. To select a file, either type the name of the file with a .dat suffix (in your current directory) into the text window at the top of the panel or select Open to bring up the Mac-like OSF/Motif File Selector (see above).
File Writing Control Panel Name of file to be written. Position the cursor in this window and type the file name, or select the Open Button for the Motif file selector.
Write Scroll bars for viewing long file names Position cursor in this window, double click with left mouse button on the word 'Title:' and type in optional descriptive title of structure.
Title: Separate causes any individual molecules to be written to the file as separate entries.
WSet causes only the working set atoms (if one is defined) to be written to the output file. Separate WSet Overwrite causes old contents of file to be replaced OverWrite with new structures, otherwise new structures are appended to the end of file. MModel P D B MModel and P D B are the two supported file formats. Write Open Quit WRITE - causes the current structure file to be written. OPEN - accesses the OSF/Motif file selection widget. QUIT - removes file control panel.
If the file name is typed into the window at the top of the file control panel, then the file will be written into the user's local directory when the Write button is picked. If a different directory is desired, then the full path name may be entered along with the file name. If a file of the selected name already exists, then the full contents of the old file will be replaced by the structure on the screen. If the Overwrite option is turned off the structure on the screen will be appended to the end of that file. While files may be written in either MacroModel (MModel) or
MacroModel User Manual Version 7.0 27 CHAPTER 2: Input Mode and General Operation
Protein Data Bank (PDB) formats, we suggest MModel format because it has better coordinate precision plus full bonding information and atomic charges. If Open is selected, the OSF/Motif file selector will appear. It is operated as described in the file reading section above.
Foreign Structure Files
It often desirable to convert molecular structures in various formats to the Macro- Model (MModel) format. Details of the MModel format are given in Appendix 5 of this manual. MacroModel has the ability to read and write PDB files directly and to interconvert SYBYL MOL2 files. PDB files can be read from within the graphical user interface. SYBYL MOL2 files must be converted using the pro- grams we provide. Currently there is no option to read or write MOL2 files from within MacroModel front-end. This is planned for a future release.
Protein Data Bank (PDB)
Protein Data Bank (PDB) is a common format for structures from crystallographic sources or from other molecular modeling programs. MacroModel converts authentic Brookhaven PDB files to MModel format using the supplied program pdbmmod. It assumes that all nonstandard residues will have connect records and that standard residues will have Brookhaven standard atom and residue labels. For nonstandard residues, the CONNCT records define atomic connectivity and bond orders. The pdbmmod program is intended for conversion of files from the Brookhaven Protein Data Bank. Many other PDB-style files do not follow the standards exactly and consequently need special treatment. So that such files can be converted, we provide the pdbmmod FORTRAN source which can be modi- fied as necessary for other PDB-like formats. The pdbmmod program is used by MacroModel for conversions whenever the PDB format is selected on the Read File panel. A related program, mmodpdb, converts MModel format files to PDB- style files and is used for PDB file writing.
SYBYL MOL2
Included are programs for converting to and from the SYBYL MOL2 file format. These programs are stand-alone applications and currently must be run from the UNIX command line. These programs are called mmodmol and molmmod and are located in the $MMOD_ROOT/run/exec directory.
28 MacroModel User Manual Version 7.0 Structure File Reading and Writing
Cambridge Crystal File
We do not have software to read Cambridge Crystal File entries directly, but we do supply a program called xraymmod which converts generic x-ray Cartesian coordinate files to MModel format. All that is required is a file having one line for each atom containing its standard elemental symbol and Cartesian coordinates (x,y,z). The format for each line of the file is A2, 3F10.5. The program xraym- mod asks for unit cell parameters interactively for use in converting the input file of atomic symbols and coordinates. Bonds are estimated from atom proximity's and all bond orders are defined as single. Thus the bonding of resultant structures should be carefully checked and multiple bonds added interactively by overdraw- ing the bonds using the DRAW button in MacroModel. xraymmod FORTRAN code is provided so that it can be modified as necessary for converting data in other formats to MModel format.
Compressed MacroModel Files
As of version 5.0 MacroModel supports a compressed file format. The BatchMin program may write certain multiple structure files in a compressed format. Mac- roModel and programs such as XCluster are able to read compressed files. There may however be occasions when users wish to convert a compressed file into a full representation. To do this we have supplied a program called mmio_convert in the $MMOD_ROOT/run/exec directory. To uncompress a compressed structure file the syntax is:
mmio_convert -f compressed.out full.out
where compressed.out is the name of the compressed file and full.out is the name of the file which will be created with a full connection table.
2.2 MacroModel 2D: X-Windows (Two-Dimensional) Operation
Upon program start-up, select terminal type 1 for X-terminal displays. Use the 2D mouse (left button for 3-button mouse) to select menu buttons and atoms. All menus are in X-windows so they can be moved, resized, pushed, popped, etc.
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Various global and substructural geometrical transformations such as rotations are available by the same mechanism used in previous 2D versions of Macro- Model. Thus global rotations can be effected incrementally using the Rot X, Rot Y and Rot Z buttons. Torsional rotations are accomplished using the ROTAT but- ton (pick 4 atoms to define the torsion and enter the desired angle). Molecular translations may be carried out using M XY. Select molecular translations, pick any atom in the molecule and then the desired position. To carry out molecular rotations, use ROTAT (pick an atom in the molecule to be rotated, then point to a blank place on the screen and answer the prompts), or ORIENT submode (where you would put the molecule to be translated/rotated into the working set - use the Mol button in ANALYZ->SETS->Mol - and then use T/R for translations/rota- tions).
With a fast network connection, real time global rotation for small molecules can be accomplished by holding the middle mouse button down inside the Main Structure Window and slowly moving the mouse horizontally (rotation around Y) or vertically (rotation around X). Real time global rotations are handled in 3D MacroModel mode by the same mouse manipulations.
Global XY Translations
Global XY translations are accomplished by holding down the right mouse button while moving the cursor vertically for Y and horizontally for X. Note that on some displays the on-screen translation of the structure may be large compared with the mouse movement, (i.e. the structure appears to move quickly). Real time global translations are handled in 3D MacroModel mode by the same mouse manipulations.
Global XY Rotations
Global XY rotations are accomplished by holding down the middle mouse button while moving the cursor vertically to rotate around the X-axis and horizontally to rotate around the Y-axis. Real time global rotations are handled in 3D Macro- Model mode by the same mouse manipulations. Note that any rotations immedi- ately update the connection table coordinates. This differs from the 3D GL mode which stores a transformation matrix for global XY rotations and only updates the connection table coordinates when certain local transformations are executed (like torsion rotations).
30 MacroModel User Manual Version 7.0 Scaling and XY Clipping
Scaling and XY Clipping
Scaling and XY clipping are controlled with the Scale and Clip buttons. To reposition all structures, use the left mouse button to pick Scale and then two positions in the Main Structure Window which define the upper left and lower right corner of the desired position. Double click on Scale to recenter and rescale all structures to fill the Main Structure Window. A similar procedure with Clip can be used to display only part of a complex structure. Clip can be used repeat- edly to clip away more and more of an already clipped structure. Double click on Clip to turn off structural clipping and return to full structure display. The Opt panel can be used to force a redraw of all on-screen structures by choosing the Update button. The Opt panel can also be used to erase, rescale to fill the screen and redraw the entire structure by choosing the Reset button, or to turn on the stereo pair display (Stereo).
X Emulators
Many X Server packages are sold for the Macintosh and PC. We have used the following packages here. This is not an endorsement of any kind for any of the products listed here. There are many alternative sources for similar products and these are included here only since we are familiar with them.
Macintosh MacX from Apple 800-776-2333 PC XVision from VisionWare 415-325-2113 Table 2. X Server Software
For more information on MacX X-terminal emulation on a Macintosh see Appen- dix 2.1 on page 121.
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2.3 MacroModel 3D: GL (Three-Dimensional) Operation
To run MacroModel on Silicon Graphics workstations, you will need Version 5.2 33DD or later of the Silicon Graphics IRIX operating system. To run the program on IBM RS/6000 workstations, you will need Version 4.1.4 or later of the IBM AIX operating system and a 3D graphics adapter that supports Z-buffering, 24-bit graphics and GL (not OpenGL). If you wish to carry out energetic tasks on remote computers, they will need to be connected by NFS to your workstation (see Appendix 3). TCP/IP network connections between MacroModel and Batch- Min can also be used but will need to be installed by your system manager. See Appendix 3.5 on page 134.
Upon program start-up, select terminal type 2 for 3D modeling on a Silicon Graphics or on an IBM RS/6000. Four windows will appear: A large main struc- ture window (blue/black background), a small Control Window (black back- ground), a vertical menu window (green/gray/green background) and a rectangular Message Window (gray and green background). See “Message Window” on page 16.
Scaling and XY Clipping
Scaling and XY clipping are controlled with the Scale and Clip buttons. To reposition and rescale all structures, use the left mouse button to pick Scale and then two positions in the Main Structure Window which define the upper left and lower right corner of the desired position. A similar procedure with Clip can be used to display only part of a complex structure. Such clipping enhances graphi- cal performance but zooming (Control Window) does not. Double click on Scale to rescale displayed structures with recentering to fill the Main Structure Window. Double click on Clip to turn off clipping and return to full structure dis- play. The Opt button provides access to the stereo pair display (Stereo) and var- ious rendering options (polytube, CPK, depth cueing, etc.).
Operation of the 3-Button Mouse
The program is controlled by the workstation mouse and its three buttons have the following functions:
32 MacroModel User Manual Version 7.0 Global Transformations
Left mouse button - pick structural atoms and menu buttons, also use as a
Middle mouse button - hold down and move mouse horizontally or vertically to effect three dimensional translations and rotations (global translations are done with the right mouse button).
Right mouse button - pick an atom to place it in the center of the screen and define it as the origin of global rotations, or depress button and move mouse for global translation. This mouse button may also be used to select a menu button for on- line help.
Mouse Button Functions MacroModel Functions Left button - Pick atoms and menu buttons; select default option to prompt. Middle button - Controls real time 3D transformations Right button - Center structure (origin of global rotation) on picked atom or translation; online Help for menu buttons.
LMR OSF/Motif Window Manager Functions Select Window Border: Left button - Resize selected window. Middle button - Move selected window. Right button - Menu for raise, lower, etc.
Global Transformations
The most common 3D modeling functions are translation and rotation (collec- tively called transformations) of the global view of the molecular structure on the screen. As noted above, the position of the structure on the screen can be con- trolled by selecting an atom with the right mouse button. By picking an atom with the right mouse button, the entire structure is translated to place the selected atom in the center of the screen. Any subsequent global rotations will also use that atom as the origin of rotation. Real time, smooth translation is effected by moving the cursor into the main structure window, depressing the right mouse button and moving the mouse. Rotations are effected similarly by depressing the middle
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mouse button and moving the mouse (the default is global, dual-axis XY rotation - vertical mouse movement gives X rotation, horizontal movement gives Y rota- tion). For Z rotation, hold the keyboard 'z' key down along with the middle mouse button.
Scale Button - Selecting Scale (upper part of Submode Options window) once and then pointing to two locations in the main structure window to define an upper left and lower right corner of a box will cause the structure to be moved and scaled to fill that box. Selecting Scale twice will cause the entire structure to be cen- tered and rescaled to fill the screen. Such a double scale can be used as a general graphical reset. It is commonly used for automatic recentering and scaling. Graphics can also be reset by choosing the Opt button and then activating the Reset button in the Opt window. The function of the Reset button is to zero the display rotation matrix and display the structure in unrotated Cartesian space.
Clip Button - Selecting Clip once and then picking two points in the main struc- ture window defines an upper left and lower right corner of a box. The parts of the structure inside this box will be the only ones to be displayed. Double Scale will cause the clipped fragment to fill the screen. Selecting Clip twice will deactivate clipping and cause the entire structure to be redisplayed.
Global Rotation - Rot X, Rot Y, Rot Z Buttons
The term Global Rotation refers to rigid body rotation of the entire content of the main structure window. The default global rotation state for MacroModel is dual- axis X,Y rotation. Holding the middle mouse button down and sliding the mouse horizontally gives Y rotation while sliding vertically gives X rotation. We use the metaphor that the middle mouse button grabs the front of the molecule which then rotates with mouse movement in a physically realistic way until the mouse button is released. For pure X rotation, select Rot X, Rot Y or Rot Z give pure Y or pure Z (controlled by horizontal sliding) rotation. Pure X, Y or Z rotation may be better to use at first, because they make it easier to get back to some previous view than does the dual-axis X,Y rotation mode. Global simultaneous X,Y rotation can be reactivated by double clicking on Rot X, Rot Y or Rot Z (Rot X and Rot Y will both highlight). Note that the origin of rotation can be changed by using the right mouse button to pick the atom which is to be the new center of rotation.
Rotation around the axis perpendicular to the screen (the Z-axis) is accomplished either by picking the Rot Z button or by depressing the keyboard 'z' key and the middle mouse button simultaneously. If the 'z' key is released, rotation will revert immediately to XY rotation.
34 MacroModel User Manual Version 7.0 Global Transformations
XY global rotation may also be selected by holding down the
Smooth, continuous rotation around the Y-axis (autorotation) is available via the keyboard left-arrow and right-arrow keys. The left-arrow key gives continuous S rotation (counter-clockwise) and the right-arrow key gives continuous R rotation (clockwise). Autorotation may be turned off by pressing the same arrow key used to start it. Rocking back and forth is available by using the
A given view (orientation) of the structure can be made the permanent orientation by activating the ViewSave button in the Opt menu. Such view saving should be done before file writing or plotting to preserve the desired structure orientation.
Global Centering and Translation - Right Mouse Button.
The origin of global rotation may need resetting to place it correctly in the main structure window. Such resetting allows molecular rotations to occur around points of interest in a molecule. This recentering operation can be accomplished in one of two ways. First, selecting Scale twice (double clicking on Scale) will cause the structure to be rescaled to fill the screen and make the center of the structure into the center of rotation. Second, by using the right mouse button to pick an atom, the structure will be translated to place the selected atom in the cen- ter of the screen and make that atom the center of global rotation. The center of global rotation is easy to see when using simultaneous X,Y rotation since it does not move.
The right mouse button is also used for smooth global translation (linear move- ment). Thus if the cursor is placed within the main drawing window and the right mouse button is depressed, all structures on the screen will translate as the mouse is moved.
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Zooming, Clipping Planes and Depth Cueing - Control Window.
In the lower right corner of the 3D MacroModel screen is a small Control Win- dow containing several lines and a small image of the molecule. In the upper right corner of the Control Window is a button marked with an 'S' (for 'Switch'). Picking this button with the left mouse button toggles the Control Window between the front view (used to control zooming) and the top view (used to con- trol the Z molecular display which is perpendicular to the plane of the screen).
3D Control Window g Control Control Rot T TR Mol TR All a a Top View SSFront View b
c f d
e
a - Toggle button to switch between Top View and Front View b - Back clipping plane c - Z-clipping slab thickness (controls separation of clipping planes)
d - Z-translation of molecule through Z-clipping slab e - Front Z-clipping plane
f - XY scaling (centered on origin atom)) g - Transformation toggle buttons. Rot T is used to Rotate a Torsion TR Mol is used to Translate/Rotate Molecules TR All is used to Translate/Rotate ALL (molecules with TR icons)
36 MacroModel User Manual Version 7.0 Torsion Angle Rotations
Front View - Any edge of the rectangular box (the outline reflects the viewport of the main structure window) can be picked with the middle mouse button (the box will turn orange) and moved with the button down to change the size of the box with analogous rescaling (zooming) of the structures in the main structure win- dow.
Top View - The two lines represent the Z-axis clipping planes and only parts of the structure between these two lines will be displayed in the main structure window. The upper line is the back clipping plane and marks the minimum Z-coordinate allowed for display. The lower line is the front clipping plane and marks the max- imum Z-coordinate allowed for display. Either of these lines can be picked by pointing to them with the middle mouse button (they will turn orange) and moved as desired to give the desired Z-slab. The upper line (back plane) has a small box- like control icon on its right end. Selecting that icon allows both planes to be moved simultaneously to increase or decrease the thickness of the Z-slab. There is one more control icon near the right border of the Control Window which allows Z-movement of the structure relative to both clipping planes. All of these icons are operated by picking them with the middle mouse button and sliding the mouse vertically with the middle mouse button depressed. Release the button when the desired view is obtained.
While the Control Window is usually displayed at all times in 3D MacroModel it can be removed using the CtrlWin button in the Opt menu.
Opt Button, Depth Cueing - Depth cueing can be turned on by using the Depth Cue option on the Opt menu. This option causes the lines of the wire-frame structural representations to smoothly blend to the background color as Z decreases. The brightest parts of the structure have the most positive Z coordi- nates and are nearest to the user. Depth cueing is operative over the viewable Z- slab as defined by the clipping planes in the Control Window (top view).
Torsion Angle Rotations
When in 3D mode torsion angles may be varied in two different ways. The ROTAT button operates identically in both 2D and 3D MacroModel to allow the user to set specific values for acyclic torsion angles. The Rot T button is the real time torsion angle control button available in 3D MacroModel and allows varia- tion of standard and several nonstandard torsion angles.
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Note that all torsion angle rotations modify the stored atomic coordinates immedi- ately and it is necessary to save starting geometries (e.g. in a HOLD box or file) if you do not want them to be lost. For recovery of the most previous (unrotated) torsional isomer, use the UNDO button.
Specific Torsion Angle Setting - ROTAT Button
Torsional rotations to provide specific values of a torsion angle are accomplished using the ROTAT button (select 4 atoms to define the torsion of interest and enter the desired angle in degrees). This operation can be carried out only on acyclic torsion angles. The button operates identically in 2D and 3D MacroModel.
Real Time Torsional Rotations - Rot T Button
Simple Acyclic Torsion Angles
Real time torsional rotations are carried out in two steps: first - the variable tor- sion is defined, second - it is selected and varied. To define a variable torsion, pick the Rot T button with the left mouse button, then pick the two atoms on the ends of the desired rotatable bond or pick the bond around which you wish to rotate. The first atom selected will be the stationary end and substituents of the second atom will rotate around the axis of the selected bond. After the second atom is selected, a thick yellow cross-like torsional icon will appear on the bond near its the stationary end. If the bond is selected then two icons will appear on the bond. To rotate a torsion, pick the torsional icon with
Realtime Torsional Rotations
a. Selecting these atoms with the left mouse button after Rot T c. resulting in structures like this:
1 H 2 N O R1 R R1 O 2 N H
b. will allow these atoms to R2 be rotated when the middle mouse button is depressed
38 MacroModel User Manual Version 7.0 Torsion Angle Rotations
the middle mouse button and move the mouse horizontally with the middle button depressed. This torsion will remain interactively variable until the middle mouse button is released. Upon release, the function of the middle mouse button will revert to global XY rotation. To re-establish torsional rotation, reselect the tor- sional icon with the middle mouse button. Global XY rotation for temporary view modification is also available by depressing the keyboard
Note that existing torsional icons may be selected at any time whether or not the Rot T button is active. Torsional icons remain available as long as the structure is on the screen. They are however not saved with structures written to disk files or placed in HOLD boxes.
Whenever a torsional icon is picked, a temporary angular monitor is created which displays the value of the torsion angle as defined by the lowest numbered atom substituents on the rotating bond (see also See “Monitoring Geometrical Changes” on page 43.).
Torsional icons may be removed individually by activating Rot T and then rese- lecting the atoms which were used to define the torsion. Alternatively they may be removed by picking the icon with the left mouse button while the keyboard
Torsion-like Segment Rotations
If the Rot T button is activated and a pair of atoms which are not directly bound is picked with the left mouse button, then the atoms on the shortest segment con- necting the selected atoms will become rotatable. A yellow torsional icon will be produced which may be selected with the middle mouse button to rotate the seg- ment thus defined.
MacroModel User Manual Version 7.0 39 CHAPTER 2: Input Mode and General Operation
Realtime Segment Rotations
a. Selecting these atoms with the left mouse button after Rot T c. resulting in structures like this: H O N R1 R2 R1 N O R2 H
b. will allow these atoms to be rotated when the middle mouse button is depressed
The torsional icon is placed along the line joining the selected atoms. This type of rotation is often used to rotate small segments of chains or rings without distur- bance of the global conformation. After such a rotation, substituents may have high energy bond angles and should be energy minimized or have hydrogens at the selected atoms deleted and readied.
Torsion-like Molecular Rotations
If Rot T is activated, an atom in one molecule is selected and then an atom in a second molecule is selected (left mouse button), then the second molecule can be rotated around the axis joining the selected atoms. The rotation is accomplished as with standard torsions by selecting the torsional icon thus produced with the middle mouse button and then moving the mouse horizontally while holding the button down to give the desired rotation. The
Molecular Translations and Rotations (Docking)
Docking is accomplished by translating and/or rotating one molecule relative to one or more other molecules. In MacroModel, these transformations may be accomplished incrementally (2D and 3D MacroModel) or by continuous move- ment in real time (3D MacroModel). As an aid to carrying out such transforma- tions, MacroModel provides several methods for monitoring the geometrical movements including specific distance/angle monitors and tests for atomic colli- sions (bump checking).
40 MacroModel User Manual Version 7.0 Molecular Translations and Rotations (Docking)
Incremental Translations and Rotations - Orient Submode
Orient submode is available for molecular translations and rotation in either 2D or 3D MacroModel. First activate the Mol button and point to any atom in the molecule to be translated/rotated. This operation loads the working set with the atoms of the molecule selected. Then choose a convenient local axis system using the DefAx button. The prompts will direct you to choose an origin (for rotations), an atom on the local X-axis you want and then any atom in the XY plane you desire. For most modeling operations, only the first two atoms thus selected are of significance because most rotations are carried out around the local x-axis thus defined. Finally, select T/R to activate translation/rotation. Keyboard commands control the geometrical transformation:
t Translate x Relative to local x-axis y Relative to local y-axis z Relative to local z-axis 0-9 Extent of translation or rotation in Å or degrees
Molecules can also be moved with respect to one another in the XY plane by using the M XY button. Hitting this button twice presents a popup which allows a selection of moving atoms, molecules and the working set. Choose Molecules and then click in the molecule to be moved. Click in a new position on the screen and the molecule will be repositioned.
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Real Time Molecular Translations and Rotations - TRMol Button
Real time molecular translations and rotations are carried out in 3D MacroModel in two steps: first - the molecule to be moved is chosen, second - it is selected and moved. To define a movable molecule, select the TRMol button with the left mouse button, then pick an atom in the molecule which is to be translated and/or rotated. The atom chosen will be the origin of any molecular rotations which are applied and should be chosen thoughtfully. A molecular icon will appear at the chosen atom as a thick, purple three-dimensional cross. Several atoms in the movable molecule can be chosen if several different rotation origins are desired. To translate a molecule in the plane of the screen, pick the desired molecular icon with the middle mouse button and move the mouse (keeping the middle mouse button depressed) horizontally for X translation and vertically for Y translation. Other transformations are available as keyboard options which are selected while the middle mouse button is still depressed. These options include:
X Pure molecular rotation around horizontal or X-axis (ver- tical mouse movement) Y or C Pure molecular rotation around vertical or Y-axis (hori- zontal mouse movement) Z Pure molecular rotation around screen perpendicular or Z-axis (horizontal mouse movement)
When the middle mouse button is released, the program automatically reverts to global rotation mode. To re-establish molecular translation/rotation, repick the molecular icon with the middle mouse button.
42 MacroModel User Manual Version 7.0 Monitoring Geometrical Changes
Occasionally, users may wish to move all of molecules which were picked with the TRMol button in unison. This is done by activating the TRAll button and then picking any molecular icon with the middle mouse button depressed.
Molecular icons may be removed with the left mouse button by pointing to the TRMol button and then pointing to the icon to be eliminated. Alternatively, hold the
Monitoring Geometrical Changes
As torsions are varied or molecules are moved, it is often helpful to monitor the changes with additional mechanisms. For this purpose, MacroModel provides quantitative monitors for atomic separations (ADist button), bond (BAngl but- ton, 3-body) angles and torsion (DAngl, 4-body) angles. These buttons are found in ANLYZ mode, GEOM submode. These monitors are updated after each incre- mental movement in 2D MacroModel and continuously in real time in 3D Macro- Model. Alternatively, nonbonded distances may be monitored by the Bump Checking options in 3D MacroModel. This latter option shows interatomic con- tacts in real time as dotted lines which are color-coded by the severity of the con- tact.
It is also helpful to monitor geometrical changes by viewing the structure in stereo or by frequently rotating the entire structure a little using the
Monitoring Specific Distances and Angles - ADist, BAngl and DAngl Buttons
There are sets of buttons in INPUT/Orient mode and in ANLYZ/GEOM mode which allow measurement of interatomic distances and angles. All of these but- tons operate in essentially the same way - the button is activated and either sets of two (ADist for interatomic distances), three (BAngl for bond angles) or four (DAngl for dihedral or torsion angles) atoms are then picked. As each set of atoms is selected, a monitor in the form of a line between selected atoms or bonds and a number will appear on the screen. This distance or angular display is active in the sense that it will be updated automatically as the geometry of the molecule is changed. In 2D MacroModel this updating is periodic, while in 3D Macro- Model the updating occurs in real time. Monitors are removed by picking ADist, BAngl or DAngl twice.
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Monitors stay active as long until they are removed. Thus once monitors are cre- ated using ADist, BAngl or DAngl, they may be used to monitor all sorts of structural variations including manual structural changes, energy minimizations, molecular dynamics runs and so on.
Bump Checking - Opt Button
The bump checking option of 3D MacroModel is used to show repulsive non- bonded overlaps between nearby atoms. It is activated by using the left mouse button to pick the Opt button and then one of two bump checking options in the popup options menu. One of these options, BumpCheck, will mark any pair of atoms closer than the sum of their Bondi van der Waals radii. The dotted line markers are color coded as follows:
Blue Sum VDW > Separation > 0.85 Sum VDW Green Sum 0.85 VDW > Separation > 0.70 Sum VDW Yellow Sum 0.70 VDW > Separation > 0.55 Sum VDW Orange Sum 0.55 VDW > Separation > 0.40 Sum VDW Red Sum 0.40 VDW > Separation Table 5. Bump Checking Color Coding
The other, BumpCheckClose, displays only contacts closer than 70% of the van der Waals radii sum. BumpCheckClose may be more useful than BumpCheck in complex structural environments having many nonbonded con- tacts.
Bump checking operates only on the parts of the structure which move during real time variations in torsion angles (Rot T button) or during real time molecular translations/rotations (TRMol button). When a yellow torsional or purple molec- ular icon is selected, MacroModel generates a list of all atom pairs between the moving fragment and nearby unmoving fragment atoms. As the moving fragment is moved, the list of atom pairs is checked continuously and any close contacts are marked with dotted lines on the display screen. To make bump checking occur
44 MacroModel User Manual Version 7.0 Structural Rendering Options
rapidly, the list of atom pairs includes only atom pairs which were proximate when the torsional or molecular icon was selected. If any part of the moving frag- ment is moved more than approximately 5Å, then the icon should be repicked to regenerate the bump checking pair list at the latest geometry.
Bump checking may be turned off by choosing the Opt button and then repicking the lit BumpCheck or BumpCheckClose button with the left mouse button.
Structural Rendering Options
In 3D MacroModel, there are four different forms of structural diagrams: wire frame, polytube, ball-and-stick, and CPK. Wire frame models are simple line dia- grams with bond order indicated by line thickness. Atom type labels are also available in wire frame mode. These diagrams are the default and provide the best graphics performance (e.g. smooth rotations with large molecules). Polytube draws all bonds equivalently as 3D cylinders which are capped and lit with a stan- dard lighting model. 3D graphics performance in polytube mode is acceptable for 250 or more atoms depending on your hardware. CPK and ball-and-stick are space-filling representations which can be rotated but are primarily useful as static drawings. The various options discussed below are selected via the options popup menu which appears upon picking of the Opt button (located in the Main Button Panel). After the desired options are selected, resume normal program operation. The options popup panel may be moved to a convenient location and left on the screen, or it may be removed by picking the Quit button.
Wire Frame Line Diagrams
Wire frame diagrams (line diagrams) generally provide the best working struc- tural representations and are the program default. These diagrams are normally displayed with bonds shown as thick lines but may be displayed with thinner lines by toggling (picking) the ThickBond option in the popup options menu (Opt button). On many X-windows 2D displays, the ThickBond option provides the best structural display. Atom labels (excluding C and (C)H) are shown by default for small molecules but the labels may be turned off or on using the ALab button in ANLYZ submode. Bond orders are coded by line thickness where single bonds are shown as the thinnest lines. Wire frame diagrams provide the most responsive graphics and the easiest atom picking.
MacroModel User Manual Version 7.0 45 CHAPTER 2: Input Mode and General Operation
Photographic suggestion: Ektachrome ASA 200 slide film, f2.8 or f4@ 1/4 sec- ond (use a tripod and cable release, shorter exposures should be avoided). This is a good option for complex structures when used with z-clipping and depth cueing. Use a dark or black background. Use the OSF/Motif Window Manager maximize icon on the main structure window or hit the "F1" key to fill the screen.
If captions are to be added, go to ANLYZ mode, GEOM submode and select the AddLb (Add Label) button. Type caption text into the popup window which appears, select OK and then point to an atom where the caption is to appear. Cap- tions will be colored the same as the atom selected and will rotate with the struc- ture. Captions are removed with the Clear button.
Polytube Diagrams - Polytube Button
Polytube diagrams show all bonds equivalently as three-dimensional cylinders which are color-coded by the atom type (or whatever other atom coloring option is in effect). These diagrams are useful because the lighting and Z-buffering make it easy to see the structure as a three-dimensional object even when it is stationary. Polytube diagrams may be displayed by selecting the Opt button and then pick- ing the PolyTube button in the popup options menu using the left mouse button. Atom labels should generally be turned off (ALab in ANLYZ mode) in Polytube mode. Polytube rendering may be turned off by selecting the lit PolyTube button (which will revert to a wire frame representation) or the alternative Ball+Stick or CPK display button.
Photographic suggestion: Ektachrome ASA 200 slide film, f5.6 @ 1/4 second. This is a good option for small molecules and shows three-dimensional structure well especially against a light background (Background button in the Opt menu). Use the OSF/Motif Window Manager maximize icon on the main struc- ture window or hit "F1" to fill the screen.
Ball-and-Stick and CPK Space-filling Diagrams - Ball-and-Stick and CPK Buttons
CPK and Ball+Stick are space-filling representations. These diagrams will rotate in real time but the rotations are not smooth with any but the smallest of structures. Thus they are generally best used as static displays. The CPK display uses 85% of the Bondi van der Waals radii for atom radii. Both options are avail-
46 MacroModel User Manual Version 7.0 Structural Rendering Options
able via the Opt panel. The diagrams may be turned off by selecting the lit Ball+Stick or CPK button. This will revert to wireframe representation. See section See “Resizing of CPK spheres - CPK Resize” on page 48. for how to resize the CPK spheres.
Photographic suggestion: Ektachrome ASA 200 slide film, f5.6 @ 1/4 second. Looks best against a light background (Opt menu). Use the OSF/Motif Window Manager maximize icon on the main structure window or hit F1 on the keyboard to fill the screen.
Stereo - Stereo button
Stereo pair diagrams of any rendering option may be selected by pressing the Stereo button in the Opt menu. After Stereo is selected, pick the StereoSize button and adjust the size of the images by holding the middle mouse button down and sliding the mouse left or right. Release the button when the desired image size is obtained. Next pick the StereoSep button to adjust the separation of the stereo pairs as desired again using the middle mouse button. The stereo pairs come up so that the left eye should see the left image and the right eye the right image. If you wish the alternative "cross-eyed" stereo, use the StereoSep button to switch the image positions. When stereo is in operation, make all selections of atoms or positions in the Main Structure Window on the right-hand stereo image (unless using cross-eyed stereo). Press the lit Stereo button again to turn stereo off.
Hardware Stereo
Hardware stereo is supported only on SGI machines. To use the hardware stereo option you need a hardware stereo-enabled machine and a pair of CrystalEyes glasses. CrystalEyes is a liquid crystal shutter stereoscopic viewing device, syn- chronized with the monitor using wireless infrared signals. For more information on CrystalEyes contact:
CrystalEyes Stereo Viewing System StereoGraphics Corporation 2171-H East Francisco Blvd. San Rafael, CA 94901 415-459-4500
MacroModel User Manual Version 7.0 47 CHAPTER 2: Input Mode and General Operation
The hardware stereo mode can be entered at any point during the operation of the program by hitting the escape (ESC) key on the top left of the keyboard. To return to normal display hit the escape key again. It is best to expand the main structure widow to full size before attempting to use the hardware stereo option as the Motif menus will not function in stereo. Although the hardware stereo mode can be used at anytime during the program operation it is difficult to accurately pick atoms or bonds while in the hardware stereo mode and so any picking (such as defining TRMol atoms) is best done before entering the hardware stereo mode.
Setting MacroModel Colors - Set Colors
The Set Colors button is available from the Opt panel. Selecting this button maps up a panel which allows the setting of any of the 21 MacroModel colors. The MacroModel color names are fixed, but the color values that are used for dis- play purposes are not. So, for example, you can set MacroModel red which has its RGB (red, green, blue) values set to 255,0,0 by default to be 0,255,0 which would make red appear green. A more realistic case might be to lessen the red contribu- tion for red to 180,0,0 making red duller. RGB values are set by using the sliders.
The full range of RGB values are accessible. Users will find this flexibility useful if they wish to customize the default color settings. Note that you may save out the current color settings to be the new default colors. When MacroModel starts up the next time it will use this new set of colors. Also, for users who create mesh files for use in VOLUM the Set Colors panel allows users to assign their own RGB values to the 21 MacroModel colors that are used in mesh files. In the past users were confined to the default 21 color values. This prevented users from display- ing volumes with colors ranging from, say, dark blue to light blue in 21 steps of blue.
In addition to using the RGB sliders to set color, users may now select from a list of named X colors. This will automatically set the RGB values for the corre- sponding MacroModel color.
Resizing of CPK spheres - CPK Resize
The Resize CPK button is available from the Opt panel. Selecting this button maps up a panel which allows the sizing of the CPK spheres. The change will only be visible when CPK rendering is enabled. The default is eighty-five percent of the Bondi van der Waals radii. Resize CPK allows the user to set this value to
48 MacroModel User Manual Version 7.0 Structural Rendering Options
range from twenty percent up to one-hundred-and-fifty percent. The small CPK setting (say 20 percent) can be used as a faster (but perhaps less aesthetically pleasing) ball-and-stick. This will rotate faster than the Ball-and-Stick rendering mode in the Opt panel.
2.4 Structure Building
Input mode of MacroModel contains many features for the semi-automated con- struction of organic and biopolymeric molecules and their complexes. Many of the elementary structure building options are described in detail in the Macro- Model Primer manual but are summarized below. Note the UNDO button recov- ers the structure from before the last construction operation and may be used to back up whenever an error is made.
Remember that molecular mechanics and dynamics are not effective methods for crossing significant energy barriers, and the structure which emerges from an energy minimization calculation will be geometrically related to the starting struc- ture. Thus, it is up to the user to choose relevant conformations for molecular modeling calculations. For flexible small molecule systems having up to a dozen torsion angles, conformational searching is advised (CSrch submode). Many such systems have a large number of low energy conformations and the global minimum may contribute only in a minor way to the average properties of the molecule. Consequently, finding most or all of the low energy structures is more useful just finding the lowest energy structure. For more flexible systems, experi- mental data must be used to help locate populated, low energy conformations.
Depending on the molecular mechanics force field you will use, your structure will need various hydrogens and, in some cases, lone pair electrons. All force fields require explicit hydrogens on heteroatoms. The table below summarizes what each force field expects:
MM2* Hydrogens on all C Lone pairs on O(sp3) MM3* Hydrogens on all C No Lone Pairs Table 6.
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AMBER* Hydrogens on C optional. We Lone pairs on S suggest hydrogens on aromatics only. OPLS* Hydrogens on aromatics No Lone Pairs OPLS-AA Hydrogens on all C No Lone Pairs AMBR94 Hydrogens on all C No Lone Pairs MMFF Hydrogens on all C No Lone Pairs Table 6.
While MacroModel will attempt to correct the lone pair protocol before an energy calculation, it is best to set it yourself using the HADD or HDEL buttons when construction of the structure is complete.
Modifying Existing Structures
The most common way of creating new structures for modeling is to modify a closely related structure. Such structures can originate from a previous modeling session, from templates in the various Input submodes of MacroModel or from some external source such as a crystallographic data base. Typically, structures of interest are saved as disk files for use in subsequent modeling sessions.
Modifications typically involve the addition or deletion of molecular substructures or conformational/configurational modifications. To add new substructures, it is often easiest to replace hydrogens with carbons (CH4 in the Organic Submode menu converts H to methyl, CH3) or with functional groups (e.g. C=O converts H to formyl, CHO). For long chains, turn on GROW, select the atom to be the grow- ing origin (Orign) and pick the sequence of groups desired from the input sub- mode menu. Turn off GROWing when you are done. For united-atom structures (lacking hydrogens bound to carbon), add hydrogens first (HADD), construct the desired structure with hydrogens, then remove the hydrogens (HDEL) when the construction is complete. Remember that all force fields use explicit hydrogens on heteroatoms. For heterofunctional molecules, construction first as a hydrocar- bon and subsequent substitution by desired heteroatoms is an effective molecule- building strategy.
Geometrical modifications include conformational and configurational changes. For acyclic structural fragments, the ROTAT or the Rot T buttons can be used to change various types of torsion angles (see ROTAT and Rot T descriptions above). Note that some torsions in rings can also be changed using the Rot T but-
50 MacroModel User Manual Version 7.0 Structure Files from External Sources
ton using a segment rotation (see Rot T description above) Moving one molecule relative to another or docking is most easily accomplished in 3D MacroModel using the TRMol button (see TRMol description above) and is best monitored in stereo.
Configurational changes can be carried out using the Invrt button in Organic and Peptide Input mode which inverts chiral centers (part of no more than one ring), acyclic alkenes (or amides, esters, etc.), or interconverts enantiomers.
Structure Files from External Sources
Molecular structures from external sources often have defects which must be cor- rected before they can be used in molecular mechanics. Structures from the Brookhaven Protein Data Bank (PDB structures) often lack hydrogens on heteroa- toms (e.g. H(N), H(O)) and occasionally do not include bond orders. In Macro- Model, all molecular mechanics force fields require hydrogens on heteroatoms. These may be added via the HADD button or may be manually drawn. HDEL will remove hydrogens only from carbon atoms unless the atoms are picked explicitly.
Bond orders originating from non-MacroModel format files should also be care- fully checked. Structures converted from or read directly as PDB format files will usually have bond orders in standard residues loaded correctly but other structures (e.g. cofactors) will be correct only if the PDB file contains the correct comple- ment of connect records. Unusual structural components should be carefully checked for correct bond orders and atom types. If you have trouble distinguish- ing double (thick) and single (thin) bonds, go to ANLYZ mode and toggle the BLab (bond order labeling) on and off.
One of the more common reasons that force field parameters are not found for new structures is that bond orders are incorrect or hydrogens are missing from some heteroatom. If an energy calculation fails because of missing parameters, look at the job.log file to see what atom numbers and types are involved (see section APPENDIX 4 on page 147) . Often, examining the offending atom graph- ically will reveal missing hydrogens or an incorrect bond order. For finding the atom by number, go to ANLYZ mode and turn on atom numbering (NUM button) or use FAtm to find a specific atom by its number.
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Manual Molecular Construction
Most of the manual methods are detailed in the MacroModel Primer manual so they will be only summarized here. First, DRAWing can be used to sketch manu- ally a desired molecule. All atoms are initially created as carbon but these may be readily changed to any desired atom type after the construction is complete. Such manually drawn molecules will be planar unless the structure is rotated before the structure sketching is complete. The user should then use the M+Z (out of the screen; toward the user) and M-Z (into the screen; away from the user) buttons to move atoms perpendicular to the plane of the screen to give a rough approxima- tion to the desired three dimensional structure. The stereochemistry of substitu- ents may also be defined in this way. After the rough geometry is created, it should be rotated or viewed in stereo (Opt button) to be sure the structure created is the desired one. Use M XY to move any atoms in the plane of the screen which appear in unreasonable positions. Then add hydrogens (HADD) as desired. Remember that molecular mechanics requires hydrogens at least on all heteroat- 2 oms and we advise using hydrogens on sp carbons as well.
For small molecules, manually linking fragments from an INPUT submode options menu is often a better alternative to drawing because it leads to three- dimensional structures directly. The general approach is to select an initial sub- structure (e.g. CH4 for a methane or CHexa for cyclohexane) and place it in the main structure window. Next a substituent is again chosen from the menu and an atom (e.g. a hydrogen) of the initial structure is picked to make the substitution. For forming rings, end-atom hydrogens can be removed and the ring closed by DRAWing a bond.
For linking two structures in the Main Structure Window to form a single mole- cule, the FUSE and CNNCT (connect) buttons in Organic Input mode can be used. FUSE replaces the chosen atoms of the first-selected molecule with those of the second-selected molecule. CNNCT joins molecules by a single bond con- necting selected atoms. Thus FUSE could be used on two cyclohexanes to pro- duce various bicyclic systems including spirocycles, decalins or bridged rings. CNNCT would be used to make bicyclohexyl or multiply connected tricyclics. Start causes the operations defined with FUSE or CNNCT to be executed. See the MacroModel Primer for examples of CNNCT and FUSE.
52 MacroModel User Manual Version 7.0 Conformationally Flexible Molecules
Conformationally Flexible Molecules
As noted above, many molecules are conformationally flexible and it is up to the user to provide low energy, populated conformations as starting geometries. For simple structures with only a few variable torsion angles, the various structures can be created by hand - often by manual torsion angle rotations (ROTAT or Rot T). It is wise to energy minimize all conformational possibilities and compute the Boltzmann population of the various states before making inferences from the modeling.
For molecules with more flexibility (up to about a dozen variable torsion angles), automated conformational searching is advised. The literature contains many reports on the utility and limitations of conformational searching, see: J. Med. Chem., 1669 (1988); J. Am. Chem. Soc., 112, 1419 (1990); J. Comput. Chem., 12, 1110 (1991). BatchMin contains a number of highly effective procedures for con- formational searching of acyclic and cyclic molecules. Such searching is a very important part of molecular modeling. In conformational searching, it is impor- tant to establish that the results are converged, i.e. that all low energy minima have been found. The best way to establish convergence is to carry out several searches with different starting geometries and show that each search produces the same set of low energy minima.
For more flexible molecules, conformational searching is not powerful to cover all conformational space, and structures produced by any method should be consid- ered only a sampling. While x-ray structures are nearly always low energy con- formations, there is no guarantee that the x-ray, solution and gas phase global minima will be the same. Structures with strong electrostatic interactions (e.g. hydrogen bonding) between nearby molecules in a crystal lattice can be distorted significantly relative to the global minimum of the isolated molecule.
Molecular Complex Construction and Docking
Building molecular complexes is easy with 3D MacroModel and begins by place- ment of molecules to be docked on the screen. For large, biopolymer systems, use of CrystalEyes hardware stereo is advised. Use the TRMol button to make each molecule independently movable by selecting one or more atoms in each mole- cule with the left mouse button. A purple cross-like icon will appear at the selected atoms. If one of these icons is then picked with the middle mouse button, it will turn orange and the molecule will translate in the plane of the screen with
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the mouse as long as the middle button is kept depressed. If the view is globally rotated (by depressing the
Rotation of the molecule around the picked atom is accomplished similarly except that the keyboard
For docking a file of structures (e.g. substrates) to some other structure (e.g. an enzyme), the following procedure can be used if the substrates are all similarly oriented. First read in the receptor. Next turn off the Delete button (to disable structure deletions) on the popup Read panel. Then open the file of substrate structures and read in the first substrate. Use TRMol to select the substrate and dock it into its binding site using the middle mouse button. Next use the DELET button to delete the old substrate molecule and then select the Read button on the popup Read panel to bring in the next substrate in the file. This procedure can be automated using the DFile button in ANLYZ mode, GEOM submode (see section 4.5 on page 88).
Renaming Facility - Renam
The button for the renaming facility is located in PEPTID mode of INPUT. Clicking on this button maps up the Rename Panel which allows a user to alter chain, PDB residue, and PDB atom information of on-screen structures.
MacroModel typically marks residues as unknown (UNK) and blanks out all the atom names in a residue when an atom in the residue is either altered or deleted. Sometimes this is not desirable.
54 MacroModel User Manual Version 7.0 Renaming Facility - Renam
Rename Panel
Select a button: Chain
Residue
Atom
New Value:
OK Clear Help Quit
Users may rename by choosing one of three methods -- chain, residue, or atom. Choosing Chain allows the user to pick a chain with the mouse and enter the new name. All the atoms in that chain (molecule) are updated with the new chain name.
Residue similarly allows the user to pick a residue (by picking an atom in the residue) and then enter a new residue name. Note that if the residue name is a PDB residue name the corresponding MacroModel residue name will be automat- ically be updated. If the residue is a non-standard residue type, the MacroModel type will be set to unknown ('X'). If the type is a standard residue, then the Mac- roModel residue field will be automatically updated with the equivalent Macro- Model residue type.
The Atom option allows the user to pick an atom to rename. Atoms are renamed an atom at a time. The user selects an atom to rename and enters the new PDB atom name. Note that renaming of an atom only affects the PDB atom name. The MacroModel atom field is not altered.
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Extended Atom Types
MacroModel handles extended atom types as defined in the atom.typ file. Upon start-up MacroModel looks in the current working directory for a file called atom.typ. If it finds one, it uses this file. If it does not find one locally, it looks in the $BATCH_ROOT directory (where $BATCH_ROOT is an environment variable specifying a directory).
The first 64 atom types in MacroModel are fixed. That is, making changes in the atom.typ file does not affect these atom types. Atom types greater than 64 that are entered into the atom.typ file will be read and used by the program.
To define an atom as one of these extended types (types greater than type 64) use the '*' button in any of the INPUT modes. This will display a complete list of all available atom types (including the base 64 types). You may select one, then pick the structure to be assigned that type. This current selection may now be used to replace any existing on-screen atom.
If you want hydrogens, you must first HADD to the on-screen atom (most likely a C atom) which you will be altering. Then replace the on-screen atom with the new type. You can not add hydrogens to atom types greater than 64; however, replacing an on-screen atom that has attached hydrogens with a new atom of type greater than 64 will not delete any of the attached hydrogens. If you wish to delete any unneeded Hydrogens, you may do so by using the DELET option.
56 MacroModel User Manual Version 7.0 CHAPTER 3 Energy Mode and Operation with BatchMin
In MacroModel, all energetic calculations are carried out using the auxiliary com- putational chemistry program BatchMin. BatchMin runs such calculations as independent batch mode tasks and consequently does not tie up the graphics device with lengthy computations which are underway. To provide interaction with the BatchMin tasks, MacroModel monitors the tasks so that both numerical and structural information may be viewed while the energetic tasks are running. Such monitoring is the default mode of operation for newly started energetic tasks; although monitoring can be broken off and reestablished at any later time. Thus as of MacroModel V5.0, users may initiate several BatchMin tasks, discon- nect from them, carry out graphical modeling operations, and periodically recon- nect to and examine the progress of each of the previously submitted BatchMin energetic tasks. As of MacroModel V6.5 there is no longer a limit to the number of atoms BatchMin may be scaled up to handle: see the BatchMin manual for details.
3.1 MacroModel Force Fields
The potential energy surface used for BatchMin energy calculations is the classi- cal one known as molecular mechanics. This is an empirical model which is parameterized to reproduce known structural and energetic data from experiment and/or quantum mechanics. The equation and parameter sets which allow calcula- tion of energy from a molecular geometry are known as force fields. In Macro-
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Model/BatchMin are equations and parameters from several published standard force fields (MM2, MM3, AMBER, OPLS). The BatchMin implementations of these standard force fields differ in various ways from the authentic force fields. We distinguish our fields from the originals by adding a '*' to the end of the force field name. MacroModel force field parameters and equations selectors are found in force field files having suffixes .fld (e.g. mm2.fld). These differences are summarized below:
Differences in force field equations
MM2* - All force field equations are identical with those of authentic MM2 from N.L. Allinger except: 1. the electrostatic equation (MacroModel uses partial charges and Coulombs law whereas MM2 uses bond dipoles and the Jeans equa- tion), 2. the out-of-plane bending equation (MacroModel uses an improper torsion while MM2 uses a pyramidalization distance - the difference being insignificant except for substantially distorted sp2 systems), and 3. the way conjugation is han- dled (MacroModel uses specific V1-V3 torsional terms for conjugated systems whereas MM2 uses an SCF pi calculation in uncommon systems).
MM3* - All force field equations are identical with those of authentic MM3 from N.L. Allinger except for those differences listed above for MM2.
AMBER* - All force field equations are identical with those of authentic AMBER from P. Kollman. The MacroModel default for hydrogen bonding uses Kollman's recent 6,12-Lennard Jones treatment (J. Comput. Chem., 12, 620 (1991)).
OPLS* - All force field equations are identical with those of OPLS/AMBER from W. Jorgensen.
OPLS-AA* - OPLSA-AA force field. This force field, developed by Professor W. Jorgenson of Yale University, is probably the best one available for condensed- phase simulations of peptides. All force-field equations are identical to those of authentic OPLS-AA (W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11225-11235). BatchMin’s implementation has been vali- dated by comparison to BOSS OPLS-AA calculations for a wide variety of organic systems. Comparisons to ab initio calculations and experiment show that OPLS-AA reproduces conformational energies well for systems for which it has been specifically parameterized. However, especially good results can be expected for proteins. The parameters have been updated to June 1999, and some
58 MacroModel User Manual Version 7.0 Differences in parameters
are as recent as December 1999. With the exception of improved charge, van der Waals and torsion parameters for sulfur in thiols and thiol ethers (G. Kaminski and R. Friesner et al., in preparation), all parameters are native OPLS-AA. The new thio parameters, which use appreciably smaller charges on sulfur and which have been validated in liquid-phase simulations on thiols and thiol ethers, signifi- cantly improve the conformational energetics of CYS and MET residues in pro- teins. In collaboration with Professor Jorgensen’s laboratory, we are working to extend the parameterization to broader classes of drug-like molecules and expect to offer a substantially enhanced version of OPLS-AA for the next release.
.AMBER94 - All force-field equations and parameters are the same as in Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I.R., Merz, K. M., Ferguson, D. M., Spell- meyer, D. C., Fox, T., Caldwell, J. W. and Kollman, P. A., J. Am. Chem. Soc. 1995, 117, 5179, with the following small exceptions. First, since in MacroModel par- tial charges are specified by bond dipoles rather than as charge values, the partial charges may differ slightly between the two implementations; these differences are typically in the fifth significant figure. Second, the atoms defining improper torsions are not specified by the AMBER protocol in situations of high local sym- metry. This may sometimes give rise to small differences in molecular energies or geometries between the two programs. Third, though the Kollman paper gives the two nitrogen types different van-der-Waals parameters, the AMBER 4.1 program uses the same parameters for both. We follow the convention of the program.
MMFF - Our implementation is identical to that described in Halgren, T. A., J. Comput. Chem., 1996, 17, 490-512; 520-552; 553-586; 587-615; 616-641. We supply both MMFF94 and MMFF94s; the latter enforces planarity about delocal- ized sp2 nitrogens. See also Halgren, T.A., J. Comput. Chem., 1999, 20, 720-729, 730-748.
Different force fields use different defaults for their electrostatic treatment (con- stant or distance-dependent dielectric) and their cutoff distances (van der Waals and electrostatic). It is possible to set such options exactly as in the authentic fields using ELECT and CUTOF buttons in ENRGY Mode.
Differences in parameters
All MacroModel force field files contain the authentic parameter set published by the original authors of the force field. In addition to these parameters are other parameters from other sources (e.g. the literature or work at Columbia). Parame- ters in the force field files are labeled as to their origin (O = original from the force
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field authors, M = modified from the original values, and A = added from some other source where no original parameter exists). They are also labeled by quality (1 = high quality final value, 2 = tentative value based on more than one experi- mental or quantum calculation, 3 = crude low quality parameter). Sources of A and M parameters are given at the ends of the lines in the force field files and recent additions to the force fields are documented in the MacroModel Technical Manual. Whenever an energy calculation (ECalc with a full print) is carried out, a listing file (jobname.mmo) can be produced which contains all parameters used in the calculation along with the origin and quality of each parameter. Note that any torsion parameter where all V1- V3 are all set to zero will not be included in the output. To include these in the listing it is necessary to include a DEBG command in the command file: see the BatchMin manual for details. This auto- matic parameter referencing feature provides important information on the quality and reliability of the calculation.
When a calculation uses low quality (quality = 3) parameters, then its results are unreliable. Conformational energy differences will likely be highly inaccurate if low quality torsional parameters are involved. Low quality stretches often indi- cate crude partial charges since charge information often originates from bond dipoles; this has particular importance if a solvation model is used. Whenever MacroModel initiates an energy calculation, a warning and the numbers of low quality of stretch, bend and torsional parameters in use are listed to the message window. An example is shown below:
WARNING - Conformational Energies May Not Be Accurate WARNING - Solvation Energies/Charges May Not Be Accurate Low quality force field parameters in use: Number of low quality stretches, bends & torsions = 1 1 8
The above message indicates that eight low quality torsions and one low quality stretch are in use in the calculation. Consequently, conformational energy differ- ences and solvation energies may be unreliable. By looking in the job’s .log file, the user may see which line(s) in the force field file is the source of the low quality parameters. Listings of the specific torsions having low quality, type 3 parameters can be found in the job’s .mmo file after an energy calculation with full printing. To make the calculation more reliable, new parameters would have to be determined to fit experimental or high quality ab initio data and added to the force
60 MacroModel User Manual Version 7.0 Differences in parameters
field file. If conformations are being compared which do not involve significant changes in the torsions having low quality parameters, then errors may not be large. See the MacroModel Technical Manual for a further discussion of parame- ter quality.
The user should always check the summary of low quality parameters in use to determine the quality of the force field for the problem at hand.
3.2 Solvation Treatment
While many molecular modeling studies are carried out without including the effect of solvent, the omission is largely one of expedient. Most experimental studies are carried out in solvent, and the solvent medium can have a major effect on molecular structures and energies. For some molecule types such as a small organic molecule with only one polar functional group, solvation does not appear to be a major determinant of conformational energies. However, for molecules having several polar functional groups, the effect of solvent can be dramatic since the electrostatically least stable structures are typically the most heavily solvated and thus stabilized in a polar solvent.
Using an explicit solvent model is one answer; however, it has its own problems. In particular, solution calculations run much more slowly because there are so many particles when hundreds of explicit solvent molecules have to be included. Furthermore, convergence is a problem in that longer simulations or different sol- vent starting configurations give different final energies. Consequently, simple energy minimization is not useful in an explicit solvent.
MacroModel uses an alternative solution model which treats the solvent as a fully equilibrated analytical continuum starting near the van der Waals surface of the solute. The model is termed the GB/SA model and is described in J. Am. Chem. Soc., 112, 6127 (1990). MacroModel is equipped with the GB/SA solvation model and parameter files are included for water (water.slv) and chloroform (chcl3.slv). Using the GB/SA model slows calculations by a factor of approximately three relative to the gas phase; however, because of the increased realism of calculations in solvent, it is suggested that the GB/SA model be used in all calculations. Solvation is controlled by the SLVNT button in ENRGY mode and by the SOLV command in BatchMin .com files.
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In calculations using continuum solvation, BatchMin uses an approximate solvent accessible area function for derivatives and then computes final energies with a more exact area function at the end of the calculation. Thus the intermediate ener- gies which are listed to the screen during energy minimization iterations will appear different than the final energies.
3.3 Convergence
One of the major errors in modeling is carrying out a calculation which is uncon- verged, i.e. gives a significantly different answer it the calculation continues or is repeated from different initial conditions. In energy minimization, convergence is not usually a problem; although there is no guarantee that final structures are low in energy relative to the actual global minimum. Conformational searching does well with structures up to a dozen rotatable bonds but is problematic with more flexible structures. When doing conformational searches, it is wise to carry out multiple searches with different starting geometries to verify that the same final structures are found. Dynamics calculations are also problematic because the time periods necessary for adequate coverage of conformational space is often much longer than appreciated. Stochastic dynamics does a better job of searching conformational space than does regular molecular dynamics, but neither method gives frequent crossing of barriers much larger that 3 kcal/mol. For this reason we suggest the use of the Monte Carlo/Stochastic Dynamics mixed-mode procedure. Convergence can be established by carrying out several dynamics simulations with different initial conditions (i.e. different starting geometries and/or initial velocities).
In any modeling study, it is up to the user to demonstrate that results are con- verged and what the bounds of uncertainty are. Unconverged results are useless.
Running Energy Calculations with MacroModel/BatchMin
BatchMin tasks are set up by one of two methods:
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Method 1 - MacroModel Energy Submode Panels. As in previous versions of MacroModel, submodes for energy minimization, dynamics, constraints, etc. are available to select desired modeling operations. For example, the default sub- mode of ENRGY is MINIMize which provides various standard methods for energy minimizing molecular structures. In “Full Structure Energy Minimiza- tion” on page 71 a protocol is given for using MacroModel to energy minimize a structure.
Method 2 - Manual Assembly of BatchMin Command Files. Many users manually create command files which tell BatchMin what to do. The BatchMin Reference Manual lists all BatchMin commands and gives examples of command files for various standard modeling operations. We suggest always using a MMOD com- mand opcode with arg1=5 in command files so that BatchMin jobs can be moni- tored by MacroModel.
3.4 Setting Up BatchMin Energetic Jobs
To run an energetic task with MacroModel/BatchMin, a starting geometry is pro- duced (usually in INPUT mode) and then ENRGY Mode is entered to define the task. For energy minimization as an example, the user would select MINIM sub- mode, choose a force field (e.g. MM2) and a minimization algorithm (e.g. PRCG) and then activate the Start button. The program will then prompt for a filename which will be used to name the BatchMin job. Generally, no suffix would be used in the filename. If no name is given, then the default filename of mmodtmp will be assigned. This name will be given to the file of commands which directs BatchMin to carry out the minimization. This file will be referred to in this man- ual as the BatchMin .com or COM file (or command file, filename.com). The filename given will also be used as the basis for the structural input (file- name.dat) and output (filename.out) files.
Running Old Command Files
Running an old COM file requires that you have an .com file on disk. It also requires that you have an accompanying, approπriate structure file either on disk or on-screen. To start up an old command file click on the Start button. When prompted to run an old or a new job, select ’Old’. If you have an on-screen struc- ture, the program will ask whether you wish to use the ’Current’ or ’Old’ struc- ture. The current structure is the on-screen structure while the old structure is the one on disk. When using an old structure file the base file name of the structure and command files must match. That is, for an old .com file called test1.com if
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you wish to use an old structure file it must be called test1.dat. If you use a cur- rent structure, MacroModel will write out a .dat file that has the same base name as the old .com file that you choose. So if you choose a .com file called temp1.com, then MacroModel will write out a structure file called temp.dat.
Examining BatchMin COM Files
After a task is defined using the buttons in ENRGY mode of MacroModel, the corresponding file of BatchMin commands (the BatchMin COM file) can be dis- played in the message window using the ComFl button and then choosing the dis- play command file option. It is good practice to examine such files to see that what is defined is what is intended. Such examination does however require familiarity with BatchMin COM files which are described in detail in the Batch- Min Reference Manual. The COM files produced by MacroModel are very simi- lar to the files shown in the BatchMin documentation but contain an additional MMOD command which activates the interactive monitoring features of BatchMin. Note that MMOD slows the batch jobs, because they frequently write monitoring data to disk. For lengthy BatchMin jobs, the slowdown can be minimized by set- ting MMOD arg1 = 5 or 10.
COM files may also be written to disk using the ComFl button. Such files may modified using a standard system editor and submitted manually for special oper- ations not easily set up with MacroModel itself. They can also be submitted with the Start button in MacroModel by specifying the job as 'old'.
Multiple BatchMin Operations - NxtOp Button
Some BatchMin tasks involve several operations which cannot be defined readily by simply activating MacroModel buttons. The problem is that MacroModel writes out BatchMin commands in a predefined order which may not be the same as that in which the buttons were selected. Other operations are mutually exclu- sive as are the various energy minimization methods (PRCG, TNCG, FMNR, etc.). The NxtOp button allows commands to be placed in the BatchMin COM file in an order defined by the user. The NxtOp button forces subsequent button selections to generate BatchMin commands ordered after any previously selected commands. NxtOp advances what we describe as the "operation level." Each operation level can have one dynamics command, one minimization command, one energy calcu- lation command, etc. MacroModel is currently dimensioned to allow a maximum of 5 operation levels. Each operation level carries out commands in the following
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order by default: Energy Calculation, Gradient Calculation, Minimization, Dynamics. If some other ordering or multiple commands of the same type is required, then a NxtOp must be used between them. For example, to carry out a PRCG minimization and then a FMNR for final con- vergence: 1) select a force field and PRCG, 2) select NxtOp, 3) select FMNR and any new convergence criteria you wish, 4) select Start. To minimize a struc- ture and then carry out molecular dynamics: 1) select a force field and the desired minimization method, 2) go to DYNMC submode and select NxtOp, 3) select the desired dynamics simulation options, 4) select Start. To carry out dynamics and then minimization: 1) select a force field and the dynamics simulation you desire, 2) select NxtOp, 3) select the desired minimization method, 4) select Start. When using NxtOp commands, it is good practice to examine the BatchMin COM file using the ComFl button prior to starting the job.
3.5 Starting BatchMin Energetic Jobs
Before starting a job, the user may wish to specify a host computer upon which the job will run. This selection is made via the Host button. If no selection is made, then the first entry listed in the hostfiles.dat file will used. As of ver- sion 5.5 the default entry is named bmin.auto. The bmin.auto entry attempts to run your job on the local host using an executable that is both appropriate to the architecture of your machine and to the size of your structure.
The default entry in the hostfiles.dat (i.e. the first item in the scrolling list you see when you click on the Host button) typicially corresponds to selecting the workstation where MacroModel is running. Other entries corresponding to scripts and/or hosts can be added. For a complete description of how to do this see APPENDIX 3 “Setting Up MacroModel and BatchMin Communication” on page 125
If remote hosts have been added to the hostfiles.dat file, a remote host may be selected from the list of available hosts which pops up after Host is selected. Use the left mouse button to pick the desired machine and then pick OK, or just double click on the desired host entry. If the user's login name on the remote host is the same as that on the local host, just press OK remote host login popup win- dow which appears. Otherwise, type the login id into the window first. Macro- Model will respond by printing a 'Connected to ...' message to the message window. If the connection fails, then the remote machine may be down,
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the user id may be wrong, remote access permissions may be insufficient or incor- rect, and/or if using the BatchMin server the server may not be installed properly. See APPENDIX 3 “Setting Up MacroModel and BatchMin Communication” on page 125 for instructions to set up remote host connections.
BatchMin jobs are initiated from MacroModel with the Start button. When selected, Start will prompt the user to select either a new or old file. Usually, a carriage return or left mouse button pick would be used to select the new file default (old files are COM files which were previously created and stored along with data files on the disk). Next the program will ask for a name. Choose a unique, one-word name which will readily identify your job (e.g. 'testjob'). If no name is given, then the default name mmodtmp will be assigned. Note that if the default is already in use for a BatchMin job you will have to explicitly enter a job name. This default name may be selected by simply clicking the left mouse but- ton in the window where the job name is to appear. The job name will be assigned to the BatchMin COM file (testjob.com or mmodtmp.com), and to the struc- tural input (e.g. testjob.dat) and output (e.g. testjob.out) data files. After the name is given, MacroModel will initiate the BatchMin task and monitor its progress automatically. If any button is selected, then monitoring will be ter- minated automatically and the BatchMin task will run without interaction. For 3D MacroModel, picking any button but Rot X, Rot Y, Rot Z, Scale, Clip or Opt will cause monitoring to be terminated and the BatchMin task will continue to run independently. Monitoring of the job may be re-established later as described below.
After MacroModel writes the COM and structural input files, the following mes- sage will appear in the message window to indicate that the BatchMin task has been submitted:
Wrote BatchMin Files. Job name:
After the BatchMin job actually begins running, BatchMin will write the follow- ing message to MacroModel which will then be displayed in the message window:
BatchMin Process Id:
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Subsequently, other energetic data will be sent automatically by BatchMin to MacroModel for display in the message window. Subsequently the structure on the screen will be updated periodically with the most recent BatchMin structure (e.g. every 10 iterations of energy minimization, finding a new global minimum during conformational searches). Such jobs can be terminated or temporarily sus- pended using the Stop button.
Except for the Rot X, Rot Y, Rot Z, Clip, Scale and Opt buttons, selecting any 3D MacroModel button will cause interactive monitoring of a BatchMin task to be broken off. The BatchMin task will continue to run as before but MacroModel will not display any data from the task. It is possible to resume monitoring of a running (or completed) BatchMin task using the Montr button. Upon selection of Montr, all available jobs will be listed to the message window and the user chooses the number of the job to be monitored. The program will then go into monitoring mode and actively display data on the selected task. The structure may be recentered using the Scale button (double click) and rotated (Rot X, Rot Y, Rot Z, etc. or middle mouse button) as necessary. When the task is com- pleted, the final structure will be left on the screen. The MFile button may be used to remove files associated with completed jobs.
If your computer system has other machines supported by BatchMin with an NFS or TCP/IP connection to your local workstation, then you can use the Host button to send the BatchMin job to another machine rather than have it execute locally. Monitoring will take place as usual. Such distributed processing is useful to spread tasks over available hardware or to put lengthy tasks on an available fast machine. Setting up the network connection is nontrivial but the system can be installed by your systems people as described in Appendix 3.5 on page 134.
For more experienced users, BatchMin jobs may be submitted manually as a stan- dard batch job. If the MMOD opcode is the first opcode in the BatchMin COM file, and the COM and all data files have the same root name, then MacroModel can be used to monitor the job even though it was started manually. MacroModel assumes the BatchMin structural input file will have a .dat suffix and the output file a .out suffix. Such COM files may be produced manually or by Macro- Model (use the ComFl button to write the COM file to the disk).
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3.6 Monitoring BatchMin Energetic Tasks
While newly started tasks are monitored automatically, MacroModel can be directed to monitor other tasks via the Montr button. When Montr is activated, a list of all available jobs (those having .m1 files in the user's area) is produced in a popup window. Jobs which are actively processing are labeled as 'running', those which are finished are 'completed' and those which have been suspended (see sec- tion 3.9 on page 69) are 'asleep'. The host on which an active job is running will also be given. Any such job may be selected for monitoring by picking (double click or pick and OK) the desired entry with the left mouse button or by typing the name of the job to the text window. If a sleeping job is selected, then the user has the opportunity to 'awaken it' and have it resume processing with monitoring.
During monitoring, the displayed structure may be rotated globally, may be scaled via options in the control window or via the Scale button, etc. Sometimes, start- ing monitoring results in a structure which is improperly centered (or perhaps even not visible). If this occurs, pick Scale twice (double click) to recenter it with rescaling in the main display window. Selecting any menu button other than Rot X, Rot Y, Rot Z, Scale, Clip or Opt will cause the program to break out of job monitoring mode. The structure remaining on the screen when monitoring is terminated will be the last one from the monitored task.
During monitoring the atoms in a structure are usually recolored by energetic gra- dient: from red representing strained, high gradient to blue representing relaxed, low gradient.
Manually produced BatchMin jobs without MMOD opcodes cannot be monitored in real time. However, the .log file can be read in via the ComFl button and the contents displayed in the message window (select the maximize icon in the upper right corner to enlarge the window and use the scroll bars). Any structures written to the job output file can also be read and viewed.
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3.7 Terminating BatchMin Energetic Tasks
BatchMin tasks may be terminated by MacroModel in two different ways which are available via the Stop button. First, the job may simply be stopped. Alterna- tively, it may be suspended (put to sleep) so that it will not use any computer time but still may be resumed at some later point. The sleep option is useful when sev- eral jobs are being manipulated and the user wants some particular job(s) to get most of the available computer time.
3.8 Halting BatchMin Tasks
To stop a job, you must be actively monitoring (see section 3.6 on page 68) that job. Upon activation of the Stop button, the program will ask if you wish to halt (default) or suspend the monitored job. If the halt option is selected, MacroModel will write a command to BatchMin (a .stp file) which directs it to terminate pro- cessing at the end of its current operation. Halting a job may not result in immedi- ate termination since further processing may be necessary to complete the subtask at hand.
3.9 Putting BatchMin Tasks to Sleep
To put a task to sleep, you must be actively monitoring (see section 3.6 on page 68) the task you wish to suspend. Upon activation of the Stop button, the pro- gram will ask if you wish to halt or suspend the monitored job. If the suspend option is selected, MacroModel will write a command to BatchMin (a .stp file) which directs it to go into a suspended state at the end of its current operation. Thereafter, the sleeping task will stop using significant computer time other than to check periodically to see if a wakeup command has been issued.
Sleeping tasks may be awakened by selecting the Montr button. After the user picks a sleeping task, MacroModel will ask if it is to be restarted (and monitored).
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3.10 BatchMin Communication File Disposition
When a monitored BatchMin job is completed, several files used for BatchMin job monitoring will be left on the disk. One of these files has the suffix .m1 and contains a listing of textual information describing the progress of the job (more complete information is often found in the job .log and/or .mmo files). The other file is a structure file with an .m2 suffix. If these files are kept in the user's directory, the job will be listed as 'completed' whenever the Montr button is selected. Such monitor files may be removed using the MFile button which will retain the structural output file from BatchMin, but will delete the .m1 and .m2 files so that the task will not be listed when the Montr button is subsequently acti- vated.
3.11 Typical BatchMin Energetic Tasks
The sections below give examples of typical modeling operations and the Macro- Model commands necessary to direct BatchMin to carry them out. Prior to these operations, it is generally necessary to select a force field (MM2*, MM3*, OPLS*, or AMBER*). The user may also elect to carry out the calculation with a solvation treatment (SLVNT button). MacroModel provides the GB/SA continuum solva- tion treatment, and water or chloroform may be chosen. The default treatment is gas phase. Changes in the electrostatic treatment (constant or distance-dependent dielectric, molecular dielectric constant) are available on the ELECT button. The default electrostatic treatment is given in the force field file (supplied as distance- dependent dielectric with MM2*, MM3* and AMBER*, constant dielectric with OPLS*; molecular dielectric = 1.0). After an energy calculation, atomic partial charges may be viewed or modified for subsequent calculations also via the ELECT button. Finally, the maximum distances over which hydrogen bonding, van der Waals and electrostatics are computed may be controlled using the CUTOF button. Default cutoff distances are 4Å for hydrogen bonding, 7Å for van der Waals and 12Å for electrostatics. The van der Waals and electrostatic cut- off distances are the center of a soft cutoff which starts at -1Å and ends +1Å.
When several energetic tasks are being carried out, it is good practice to use the Reset button to zero out all previous commands unless similar energetic tasks are desired.
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If you have several host computers on which BatchMin is installed and they have NFS network connections to your workstation, you may select the host upon which the job is to run using the Host button (e.g. in MINIM orDYNMCsub- mode). If no host is selected, then the job will run on the first host in the host- files.dat file where the available host computers are defined.
In the descriptions which follow, optional button selections are given in square brackets ( [ ] ) and denote operations which may not be necessary for particular modeling tasks.
Energy or Gradient Calculation
Button Description of operation
MINIM Select energy minimization submode.
ECalc Select molecular mechanics steric energy calculation, printing option available for detailed energetic listings to the job .mmo file or GCalc. Select gradient (total derivative of energy) calculation.
Start Choose new job and assign a name to the job.
MacroModel will automatically initiate the job on the selected host. Output is to the MacroModel Message Window and (if print is selected on ECalc) to the BatchMin job .mmo file.
Full Structure Energy Minimization
Button Description of operation
MINIM Select energy minimization submode.
PRCG Select Polak-Ribiere conjugate gradient minimization. Best general method
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or TNCG Select truncated Newton conjugate gradient minimization. Good for molecules up to 250 atoms with large gradients. Good for large all- atom structures.
or FMNRSelect full matrix Newton Raphson. Good for molecules up to 250 atoms which have been previously minimized to a gradient <1.0 kJ/mol- Å. Use the linesearching option for problematic structures with signifi- cant gradients. Alternatively reduce the gradient more using PRCG or TNCG, then try FMNR again.
[CCrit] Reset convergence criterion, default is 0.05 kJ/mol-Å.
[It/S] Reset total number of iterations (default = 500 for PRCG). Set to a larger number (e.g. 5000) for large, flexible molecules.
Start Choose 'new' job and assign a name to the job. MacroModel will automatically initiate the job on the selected host. Output is to the MacroModel message window and the final structure will be writ- ten to the
[VIBR] Vibrational mode visualization. The Vibrational mode visu- alization command allows the animation of molecular vibra- tions. VIBR generates a MacroModel multistructure output file that can be animated using either the ANLYZ->GEOM- >AutoR or the ANLYZ->GEOM->Movie option in Macro- Model. VIBR is only allowed on minimized structures unless Debug switch 211 is set. NOTE: Use the option "col- oring by energy" in MacroModel to activate a circular color- ing scheme (red, orange, yellow, green, blue) that is used to help separate the animated normal modes visually.
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Substructure Energy Minimization
Substructure calculations are used to carry out molecular mechanics on small parts (substructures) of some larger structure. With the 1000 atom version of BatchMin (bmin1K), you can carry out molecular mechanics (or dynamics) on any 1000 atoms of some larger molecule having up to a total of 5000 atoms. The 1000 atom limit includes both the substructure itself and any shells of atoms which are restrained at their original positions.
[SDLP] The Saddle point Search (SDLP) is an automated local conformational search that looks for saddle point structures in the proximity of a minimum energy structure. It's basic idea of mode-following is to move uphill on the potential energy surface along a ravine starting at a minimum, toward a saddle point. SDLP can be instructed to follow multiple modes, and each mode is followed in both directions.
Button Description of operation
SUBED Select substructure editor submode
Subs Turn on selection of the substructure of freely moving atoms.
SelRs Select substructure atoms by residue (for biopolymers with resi- due designations) by pointing to any atom in the residue. Selected atoms will be recolored white.
or Atm Select substructure atoms individually. Selected atoms will be recolored white. Reselected atoms will be removed from the sub- structure and recolored as originally.
Shel1 Turn on selection of the shell of atoms to be anchored by a har- monic restraining force at the periphery of the freely moving sub- structure. The restraining force constant may be changed from the program default at this point.
SelRs Select restrained atoms by residue (for biopolymers with residue designations) by pointing to any atom in the residue. Selected atoms will be recolored orange.
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or Atm Select restrained atoms individually. Selected atoms will be recolored orange. Reselected atoms will be removed from the shell and recolored as originally.
or Dist Select restrained atoms by their distance from substructure atoms (by number of bonds or number of Angstroms).
[AddIA] Add isolated atoms - useful if Dist/bonds used.
[RemIA] Remove isolated atoms - useful if Dist/Angstroms used.
EdgeD Edge display. Display only the periphery of the restrained atoms and the other atoms which will be totally ignored in the calculation. Use Atm to make any necessary changes to complete desirable substructures (to cre- ate intact amide bonds, etc.) within the outermost restrained atom shell.
[FxCol] Recolor atoms permanently by the substructure/shell coloring scheme. Note, if this option is not chosen, then the user will have to re-enter SUB ED submode to see color- coded substructure/shell atom selections.
[SBCFl] Write/Read .sbc (substructure/constraint) file. This option is often used in the Write mode to save substructure and shell selections for a given molecule. It is wise to use the structural WRITE button to save the structure in the same orientation as used in creating of the .sbc file.
MINIM Select energy minimization submode. On leaving SUB ED submode, atom colors will be reset to their original hues unless FxCol had been selected in SUB ED.
SubsM Turn on substructure minimization option. Then carry out the energy Energy Minimization with Constrained Torsion Angle(s)
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To carry out energy minimizations or dynamics with constraints, it is best to adjust the internal coordinate (e.g. a torsion) to a value close to that required by the constraint. For a torsion angle, this may be accomplished with the ROTAT button or by attaching a dihedral angle monitor (DAngl) to the angle of interest and then rotating around the bond to the desired value using Rot T (3D Macro- Model).
If one or more torsions are to be constrained simply at their current values, then select FxTor in MINIM submode and then pick the BOND(s) to be constrained. Next choose a method (e.g. PRCG) and Start. Repicking FxTor will remove the constraints.
CNSTR Go to constraint submode.
[Reset] Remove any previously entered constraints.
C Tor Pick set(s) of 4 atoms which define the torsion angle(s) to be restrained. The force constant default should be large enough that final angles are within a degree or so of the desired angle. For other force constants, select DefFC before C Tor.
[SBCFl] The user may wish to save the constraints chosen for subsequent modeling operations by writing a substructure/constraint (.sbc) file. The structure should also be saved using the WRITE button.
MINIM Go to energy minimization submode and carry out the energy min- imization as described in section 3.5 on page 65.
Molecular, Stochastic Dynamics And Mixed Mode
The commands below are for carrying out a simple dynamics run at constant tem- perature with computation of average enthalpy. Structure sampling during the run is optional. It is assumed that the starting structure has been energy minimized to a low gradient (section on page 71). If the structure 'blows up' (due to accumula- tion of excess kinetic energy), it is likely that the starting geometry is high in energy relative to a nearby energetic minimum. The best remedy is to equilibrate the structure by carrying out an additional simulation with a small timestep (e.g. 0.1-0.5 fs).
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DYNAMC Go to dynamics submode.
MDyn Select molecular dynamics, or SDyn stochastic dynamics (best choice, generates the Gibbs ensemble). If you take the Automatic Setup, then you will get 10 ps of dynamics with SHAKE using a 1.5 fs timestep. Adjust SimuT for a longer or shorter total simulation, and Start the job.
MCSD Select mixed mode. This automatically turns off MDyn, SDyn and SHAKE if any of them are on. You currently can not use SHAKE with mixed mode.
Mols Handles Variable Molecule Selection for Translation/Rotation. Molecule Selection for use with Monte Carlo portion of Mixed Mode. Can be used to allow a molecule to rotate/translate during a Monte Carlo step. This command should be useful in doing configurational/conformational searches of complexes. In particluar, given a docked bimoleculer com- plex, MOLS can be used to translate and rotate the smaller molecule within the binding site to look for possible binding geometries.
The user then chooses to either rotate/translate a molecule around the picked atom or around the molecule's center during Monte Carlo. Mini- mum and maximum rotational and translational also may be entered. The user can then repeat the process of adding MOLS commands (i.e. adding molecules) by selecting another atom in the molecule of interest.
Note that molecules to be translated/rotated around the center of mass are marked with yellow, and those to be translated/rotated around the chosen atom are green.
InitT Set the initial velocities to correspond to the desired simulation tempera- ture (typically 300 degrees K).
[FinlT] Set the final temperature for gradual warming or cooling. We typ- ically use this option only for simulated annealing.
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SimuT Set the bath temperature of the constant temperature (degrees K) dynamics run. This temperature is typically the same as that set with InitT.
TiStp Set the timestep. Without SHAKE, use 0.5-1.0 fs. With SHAKE use 1.0-1.5 fs. If structures tend to blow up, use 0.1-0.5 fs. The longer the timestep, the faster in time the simulation will run; however, long timesteps often make the numerical integration algorithm fail to conserve energy. If the molecule has lone pairs, they should be removed or the timestep should be reduced by 50%.
TiTot Set the total simulation length in picoseconds (ps). Depending on what is desired from the run, this may range from 1-10000 ps. If the job is monitored, the average temperature and energy will be displayed in the message window every 1-25 ps (depending on the value of TiTot).
SHAKE Take the default to constrain all bond lengths to hydrogen and lone pairs.
[Sampl] Save structure periodically to the output file during the simula- tions. Sampled structures may be used for a creating a movie (Movie in ANLYZ mode) or for conformational searching.
[Host] Select the desired computer for the lengthy BatchMin dynamics simulation.
Start Initiate the BatchMin dynamics task.
Conformational Searching - Monte Carlo Method (MCMM)
Below are given the necessary commands to use MacroModel to carry out a sim- ple Monte Carlo conformational search. It is assumed that a reasonable, energy minimized starting geometry is on the screen and that the structure is not too com- plicated. Very complex structures require more direction from the user in contrast to simple tasks (<10 variable torsion angles) which are set up automatically.
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CSRCHGo to conformational search submode.
MCrlo Select Monte Carlo conformational search. Take the normal search option which will set up all variables automatically for simple problems.
MCSM Monte Carlo Single Minimum. Allows user to enter MC Single Mini- mum criteria (number of cycles, the starting temperature, and the final temperature). To have MacroModel actually generate an MCSM com- mand, a minimization method must be chosen. If you do not, then no MCSM command will be generated. The minimization method may be chosen before or after MCSM is selected.
[Close] Show ring closure bonds (dotted lines) for cyclic structures. If you wish to remove a closure bond, pick the old closure bond with the left mouse button. New closure bonds are added by picking the desired bonds simi- larly. If you change a closure bond, you will probably have to change the variable torsion angles as well. Note that any ring with a variable torsion angle must have a closure bond.
TBond Show variable torsions. Like ring closure bonds, these may be added or deleted by picking them with the left mouse button.
[Mols] Used to select molecules for translation and rotation (multimolecular systems, docking searches).
[LMCS] The Low-Mode Conformational Search is an automated conformational search based on the so-called Low Mode Search procedure developed by Kolossvary and Guida (J. Am. Chem. Soc, V. 118, No. 21, pp. 5011-5019). Setting up an LMCS does not require the selection of torsional rotations (TORS), nor opening of rings via the Close button. As of MacroModel V6.5 LMCS allows the simultaneous use of explicit torsional rotations (TORS), molecular translations/rotations (MOLS), and opening of rings (Close).
[Symtry] Define symmetrical atoms for the purpose of distinguishing confor- mations. Carboxylate oxygens and some phenyls are automatically done.
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Cmpre Show atoms which will be superimposed for the purpose of detecting duplicate conformations. Picking atoms toggles them in and out of the superimposition set.
Chirl Show atoms with chirality constraints. Picking atoms toggles them in and out of the set. All chiral centers should be selected.
MINIM Go to energy minimization submode, choose a force field, a minimiza- tion method, and Start the job (see section 3.5 on page 65).
3.12 FFVIEW: Force-field parameter viewer/editor
The FFVIEW button in the ENRGY mode allows access to a panel which can be used to examine all the interactions present in an energy calculation. To use this panel an energy calculation with a full listing of all terms (see ECALC) must be performed on the structure of interest. The FFVIEW button can then be used to display the main panel of the parameter viewer. There are three sections to this panel. The top section contains the main control buttons. The Open button allows access to a file selection box which will display all the .mmo files in the current directory (the .mmo file is created by the Ecalc with a full listing and contains information about all the interactions). Choosing a file (by double-clicking on the file name) will start the process of reading the .mmo file and MacroModel will also read the corresponding .out file and display the structure in the main struc- ture window. The Quit button is used to dismiss the edit facility.
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Open Quit
Interactions: Stretch Bond Angle Torsion Angle Improper Torsion SA Solvation GB Solvation
Van der Waals Electrostatic
The middle section of the main panel contains a push-button for each type of interaction. These buttons will be inactive until a .mmo file is read and then only those buttons corresponding to interactions which exist in the .mmo file will become active. For example if the calculation is performed without a solvent model then the button associated with solvation will not become active. Clicking on any of the push-buttons activates an interaction display panel described in detail below.
The lower section of the main panel is used to display messages which report errors and the progress of the file reading.
Interaction display panels
All the panels have a similar layout which is illustrated by the diagram of the stretch interaction panel shown below. A number of interactions may be examined at once. The panels are dismissed by clicking in the Done button in the top right of the panel.
80 MacroModel User Manual Version 7.0 Interaction display panels
Bond Stretch Interactions. Done
1 2 Stretch Energy: 0.02800 Force Constant: 337.00000 1 7 2 3 Actual Length: 1.45350 Ideal Length: 1.449000 2 39 0 3 4 Parameter Origin: Original Paramater Quality High 3 6 4 5 Parameter Alternate: United Atom Field Charges 4 9 Parameter Comment: C-N(sp2),UA Charges
Pick from MacroModel Sort by Energy Show: All Parameters Show Force Field
All panels have a scrolling list of interactions on the left hand side of the panel. Each of the members in this list are the numbers of the atoms involved in the inter- action. For example two atom numbers are displayed for bond stretch interactions, three atoms for a bond angle etc. At all times one of the interactions in the list is highlighted and the remainder of the panel displays information about this interac- tion. In addition to this a marker will be displayed on the structure displayed in the main structure window. For example for a bond stretch interaction a purple dis- tance marker is drawn between the two atoms in the stretch, for electrostatics a green dashed line is drawn between the two atoms and so on. The information about the interaction currently selected displayed in the right hand portion of the panel is for display purposes only and cannot be edited. Note that distances dis- played for non-bonded interactions in MM2* and MM3* may differ from the actual distance between the two atoms (which will be displayed in the structure). This is because a 8.5% offset is applied to hydrogen atom C-H bonds before non- bonded interactions are calculated with the MM2* forcefield. At the bottom of the interaction panel are a number of additional controls. The Pick from Macro- Model toggle button allows toggling of the ability to select interactions by picking the participating atoms on the MacroModel structure. If the atoms picked do not correspond to an interaction in the list then the bell will sound. Although several interaction panels may be displayed at one time only one may be actively picking. When the Pick from MacroModel button is turned on it will be toggled off in any other panels which are be currently displayed. When a new panel is first made vis- ible (by clicking on the interaction push-button in the main control area) the Pick toggle will be on. Note: when the "improper" torsion panel is being used then the improper torsion interactions are selected by picking the "central" atom (that is the second atom of the four) on the MacroModel structure.
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When the interactions are first displayed in the scrolling list section it is in the order in which they were generated by the energy calculation. The Sort by Energy toggle will display the list with the largest (or most positive) interaction at the top of the list and the smallest (or most negative) interaction at the bottom of the list. Note that when changing the ordering of the list in this way the current selection is always changed to be the first member of the list.
For interactions which have a "Quality" field associated with them (stretch, angle, torsion and improper torsion) the Show: option menu is present at the bot- tom of the interaction display panel. This menu allows selective display of the interactions based on the value of the quality field. There are four entries in the Show: option menu: All Parameters, High Quality, Medium Quality and Low Quality. For example choosing Low Quality will cause only those interactions which have low quality force-field parameters associated with them to be dis- played in the scrolling list. With the graphical feedback this is a quick method for identifying and evaluating low quality force-field parameters.
Viewing the force-field
For the stretch, bond angle, torsion angle and improper torsion interactions the Show Force Field button is present at the bottom right of the interaction display panel. Clicking on this button will display the force-field panel. The force-field is displayed in a scrolling list with a single line highlighted. This highlighted line corresponds to the parameters for the interaction which is selected in the interac- tion display list - the two panels are synchronized so that as the selection in the interaction display list is changed then the selection in the force-field panel will also change to reflect the relevant line of the force-field. In practice there is little advantage in viewing the force-field from this panel unless one intends to edit the force-field (see next section) as most of the information about the parameters con- tained in the force-field is displayed in the main part of the interaction display panel.
Editing the force-field
If a force-field file is present in the current directory it will be read and displayed otherwise the program will search in the directory $MMOD_ROOT/run/mmdat. This is also the procedure used by the energy calculation. If the user does not have write permission for the file which is read, then the name of the file in the force- field panel will have "Read Only" appended to it and the editing buttons at the bot- tom of the panel will be inactive. In this case the force-field panel can only be used for viewing the force-field. If the user does have permission to write to the
82 MacroModel User Manual Version 7.0 Editing the force-field
force-field file the panel provides some simple tools for editing the file. Note that the program does nothing to validate the format of any changes made: that is totally the responsibility of the user. For this reason we suggest that any editing of the force-field is done only on a local copy of the file.
Clicking on the Edit button will display a further panel which contains the cur- rently selected line of the force-field file in a editable field. Editing can also be accomplished by double clicking on the currently selected line. The "insert" but- ton is used to insert a blank line in the force-field file at a point above the currently selected line in the file and the Duplicate button will insert a copy of the cur- rently selected line. Finally the Delete button is used to delete lines from the force-field file. When the desired changes have been made to the force-field the Save button can be used to write them back to the force-field file and all subse- quent energy calculations should reflect these changes. If the Save button is not used before the panel is dismissed the user will be asked to confirm that they really want to exit without saving the changes to the force-field.
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84 MacroModel User Manual Version 7.0 CHAPTER 4 Analyze Mode
This chapter describes many of the features available in the Analysis mode of MacroModel. Analysis mode is entered by selecting the ANLYZ button from the Main Button Panel.
ANLYZ mode contains but is not limited to the following features:
• Internal Coordinate Monitors • Atom/Residue Numbering and/or Finding • Averaged Atom Positions (Centroids) • Multiple Conformation Filtering • Multiple Substrate Docking (via a structure file) • Contour Panel (Ramachandran Plots) • Plotting Torsion Angle versus Energy • Structure Plotting • Boolean Operations on Atom Sets • Volume Boolean Operations on Molecules • Ribbon Diagrams • Movies
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• Hydrogen Bonding
4.1 Internal Coordinate Monitors - ADist, BAngl, DAngl
Values of internal coordinates (interatomic distances, bond angles and torsion (dihedral) angles) can be obtained in GEOM submode. These measurements are made either periodically (2D version) or in real time (3D version), so the monitors reflect any changes made in the geometry of the structure. Repick the ADist, BAngl or DAngl to remove the monitors. See “Monitoring Geometrical Changes” on page 43.
4.2 Atom Numbers - FAtm, NAtm, FRes, NRes, Num, Clear
It is often useful to display the atom numbering system of the molecule or to find particular atoms by their numbers. To see the entire molecule with numbers on every atom use the NUM button. If the NUM button is selected a second time, then molecular numbering scheme will be used in which each molecule has its own numbering system. The third time NUM is selected, numbering will be turned off.
To find the number of particular atoms along with their MacroModel atom types (see Appendix 4), activate NAtm and then pick the atoms of interest. To get resi- due information, activate the NRes button and pick any atom in the residue of interest.
To find which atom in a structure corresponds to some particular number, activate the FAtm button and then enter the desired atom number. It will be marked on the screen and the program will ask if you wish to recenter the view on that atom. Such recentering is often useful when you wish to see portions of a large molecule in the vicinity of the chosen atom (use the Control Window ZOOM feature to move in on the area after the recentering). Similar finding and recentering is available for given residue numbers (FRes button).
The Clear button removes all labels.
86 MacroModel User Manual Version 7.0 4.3 Textual Captions - AddLb
Textual information or labels may be added to the screen usually for display pur- poses using the AddLb button. After selecting the button, a popup window appears. Move the cursor into the text window, type in the desired caption, and select the OK button. If solid renderings (CPK, polytube) are used, begin the cap- tion with a series of spaces to offset the text from the structure. Next pick the atom(s) in the structure to which the caption is to be attached. Captions rotate with the attached atom and are colored the same as the atom.
The Clear button removes all captions and any labels.
4.4 Averaged Atom Positions or Centroids - AveAt
Sometimes the user may wish to indicate positions other than those where atoms are found (e.g. the center of a ring). Such positions may often be defined by the averages of positions of selected atoms. For example, the bond midpoint is the average position of the two bonded atoms. The center of a ring is the average position of all the atoms of the ring. Such positions may be defined using the AveAt button.
Select AveAt and then pick two or more atoms (purple markers will appear on the atoms as they are selected). After the atoms whose positions are to be averaged have been selected, press AveAt again and a green average position marker will appear. Continue picking atoms and the AveAt button to produce other average position makers as desired. These positions may be picked subsequently just like atoms and used for measuring internal coordinates (ADist, BAngl, DAngl) and for carrying out superimpositions.
Pick AveAt twice in a row to remove average position markers.
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4.5 Multiple Conformation Filtering - Filtr
Given a file of multiple conformations a user may filter out structures based upon specific selection criteria. These criteria may be combined in Boolean AND and OR operations (discussed later). A user may also wish to get data about a particu- lar characteristic (like a torsion angle) for all the conformations in the file. This data is presented graphically to the user and can be used to preview selected crite- rion before processing a file.
To access the filter panels, click on the Filtr button located in the GEOM sub- mode of ANALYZ. This will create a set of panels (see diagram below) for this purpose. The top panel is the Filter ControlFilter Control panel and is used to perform operations common to all the filter panels. These operations include reading files, writing tabular data, and creating new filter panels as well as other operations.
By default one filter panel (called Filter 1) is created and positioned below the Fil- ter Control. A maximum of up to five filter panels may be created (Filter 1, Filter 2, etc.). Each panel provides the ability to specify selection criteria of the follow- ing types -- Energy, Distance, Bond Angle, or Torsion Angle. A criterion may be modified and previewed using the items in the bottom half of a filter panel. The two scrolling graphs at the top of each filter panel are used to graphically preview a selection.
A typical application of the Filter Panel is to filter structures saved during a molecular dynamics run. For example to examine rotation around a bond one would first select the Open or Read buttons from the Filter Control to read in a reference structure from the file of structures saved during the simulation. Then choose Torsion from Filter 1 and pick the four atoms which define the torsion using the left mouse button. Hitting Preview Selection will query the file and create a graph of the value of the torsion against structure number. The distribu- tion of angles can be examined and used to choose a criterion for further filtering. If you wish to select all structures which have the torsion between -120 and 0 degrees, then enter -120 in the Minimum value field and 0 in the Maximum value field. Clicking Start on the Filter Control will start processing the file and will retain only those structures which meet the criteria specified. The saved structures will be written to the file named in the Output field or written to the screen if this field is blank. Statistics on how many structures in the file meet the criteria during the filtering will be displayed in the Filter Control window.
88 MacroModel User Manual Version 7.0 Filter Control Input Mem Map Reset Total: Output Num Accepted:
ReadRead Open Restore Tab Data Start New Panel Dummy Atoms Help Quit All
Filter 1
Energy 94.423 106.9 Torsion Minimum94.423 kJ/Mol BA 2 5 7 9 10.000 90.0 Bond Angle Maximum 106.982 kJ/Mol Distance
Energy
Delete Selection Preview Selection Quit
It is possible to specify multiple criteria for filtering. Within each panel these cri- teria are treated as AND conditions. In this case all constraints must be met for the structure to be considered to have passed the filter. For example, for the results of conformational searching one may wish to locate structures which are hydrogen bonded. One could enter a distance constraint between the donor H and the acceptor O with a maximum value of 2.5Å, and an angle constraint between N-H...O with a minimum of 90°and a maximum value of 180°. When filtering is carried out using these criteria only those structures which meet both these crite- ria (and therefore can be considered to have a hydrogen bond) will be accepted.
If one wants to also search for the presence of a different hydrogen bond then another filter panel is generated using the New Panel button on the Filter Con- trol. Similar constraints can be entered into this panel for another hydrogen bond. When two or more panels are up the constraints are first ANDed within each panel, then the results of each panel are ORed with the results of the other panel(s). In this case if a structure meets the criteria in any of the panels then it will be accepted.
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In addition to the displays available in the Filter mode itself, data can be generated for display in other packages (e.g Cricket Graph) or for construction of tables. The Tab Data button on the Filter Control can be used to create new files con- taining tables of the values of the constraints specified for every structure in the file. For the XYPlot option the file is generated in tab-delimited column format with one column for each constraint specified in all the filter panels and one row for every structure on the input file. The histogram format will create a file which has the data collected into histograms representing the number of occur- rences within a number of bins.
Further documentation is available in the on-line help of the filter panel which can be accessed by hitting the Help button on the Filter Control.
Filtr contains the functionality of the 3D-search (3DSch) facility which was introduced in MacroModel V3.5.
4.6 Multiple Substrate Docking via a Dock File - DFile
If a user has a file of substrates which are all oriented in the same way which he or she wishes to see docked in a given receptor, the DFile button provides a conve- nient method for doing this. First, read in the receptor using the READ button as usual. Then select DFile and enter the name of the file containing multiple sub- strates for docking to the receptor. After the first substrate is read in, use the TRMol (3D MacroModel) to select the substrate and then use the middle mouse button to dock the substrate as desired. Next, reselect DFile and re-enter the sub- strate file name. The first substrate will reappear. If the DFile button is then selected repeatedly, the substrates in the file will successively replace one another in the binding site of the receptor.
4.7 Dot Surfaces - SURFAC submode
Van der Waals or solvent accessible dot surfaces are operate in both the 2D and 3D versions of MacroModel. These surfaces operate as they did in previous versions of MacroModel. Note however, that the surfaces are not modified during torsional rotations (Rot T) or during docking operations (TRMol). If such operations are used with dot surfaces active, the surfaces should be removed (repick VDW or
90 MacroModel User Manual Version 7.0 Slvnt in SURFAC submode) and regenerated after the Rot T or TRMol opera- tions are completed. In the 2D version of MacroModel the dot surfaces are not displayed during realtime rotation of the structure but will be redrawn after the mouse button is released.
An accurate numerical area-calculating routine is accessible via the Area button. It operates either on the full structure or on the working set and a variable probe radius is provided. A probe radius of 1.4Å generates a solvent-accessible surface area for water. Calculated areas are accurate to better than one percent.
4.8 Contour Panel (Ramachandran Plots) - Cntr
This panel is typically used to display Ramachandran plots (.grd files) that have been previously generated by BatchMin. These are a contour diagram which rep- resents the variation of energy with respect to two torsion angles in a structure. The Contour Panel, however, is not restricted to display of Ramachandran plots but can be used to display contouring for any suitable data. The .grd file format is described in the appendix of the BatchMin manual.
To create the data for a Ramachandran plot use the DRIV button in the ENRGY mode. After clicking on the DRIV button a pop-up menu will appear which allows the selection of driving one or two angles. Only data from the driving of two angles can be displayed in this version of MacroModel. Select the angles to be driven by choosing sets of four atoms and specifying the starting value, the final value and the increment for the angle. Then choose a minimization method (e.g. PRCG) and Start the job. The progress of the calculation can be monitored as the energy for each angle will be reported to the Message Window. Note that for small angle increments, a large number of energy calculations may be required.
When the BatchMin job is complete access the contour panel by clicking on the Cntr button located in the GEOM submode of ANALYZ. Enter the name of the .grd file in the Grid File text field or use the Open button to select the file with the standard Motif file selector.
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Contour Panel
Grid File
Minimum Energy:
Maximum Energy: 10
Number of Intervals
Label Plot Help
Process Open Quit
Color Code Legend:
The Contour Panel has two main fields, a graphics display area on the left and a control area on the right. The control area has the following fields:
Grid File Enter the name of the grid file to be viewed here Minimum The minimum value of interest in the grid Energy Maximum The maximum value of interest in the grid Energy Number of The number of contour lines to be displayed Intervals Table 7. Control Area Fields
92 MacroModel User Manual Version 7.0 Label Annotate contour map with text Plot Generate Postscript plot file Help Display help panel Process Generate map based on current settings Open Display file selection panel Quit Exit panel Table 8. Contour Panel Buttons
Color Code Legend: Associates color of map contour line with interpo- lated energy value.
After having read in a grid (.grd) file one can explore the map and correspond- ing structures by depressing the middle mouse button over the Ramachandran map and moving the cursor; the program interactively updates the on-screen struc- ture. While the mouse button is depressed the energy value at the position of the cursor is displayed on the top right side of the plot, while the values of the angles on the Y and X axes are displayed on the top left and bottom right respectively. As an aid to the interpretation of the map, cross-sections for each cursor position are shown on the top and right of the map. These allow the user to establish where the low energy regions of the map and to get a visual representation of the curvature of the energy surface at any point.
The lowest energy point in the plot is represented by a small blue square. Adjust- ing the maximum and minimum values of interest in the data and the number of contour lines to be displayed allows the important features of the energy surface to be highlighted. After these values are changed, click on the Process button to re-display the plot with the new settings.
Annotation of the Ramachandran map and Postscript plotting are also supported:
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To label the plot pick the point on the plot where you wish the text to be displayed and type in the desired label. The text will appear where you picked the map. To move the text, pick the lower left corner of the first character with the left mouse, hold the mouse down and drag the label to the new location. The string will not be displayed while being dragged but will reappear when the drag is completed. To delete the label drag the string off the map and release the mouse button.
To create a postscript file press the Plot button. You will be prompted to choose an image style, either centered on an 8.5x11 inch paper (for direct Postscript plot- ting) or not centered (for inclusion in Microsoft Word document). Next, you will be prompted to choose a color space (color, greyscale, or black and white). Lastly, you will be prompted for the name of the plot file. A postscript file of that name will be created. The postscript plot will be the same size as the contour map on the screen (to enlarge the plot, enlarge the window on the screen).
4.9 Plotting of torsion angle - energy profiles - Plot1D
The Plot1D button allows access to a panel which displays torsion angle - energy plots from data stored in .grd files. The .grd file can be generated using the DRIV button in ENRGY mode. The data displayed is usually from a "drive" of one dihedral angle although this panel can also be used to display a slice from the results of a two-angle calculation.
Main Controls
The left hand portion of the Plot1D panel contains buttons will allow the user to control the display of plots. The buttons function as follows:
94 MacroModel User Manual Version 7.0 Main Controls
Quit Open PostScript Tabular Data 1D Slice Angle Plot Display Area
Energy
Absolute Energy Relative Energy
Quit - this will dismiss the panel.
Open - Open presents a standard file selection box which will display any .grd files calculated using the DRIV button. When a file is opened data in the full range of the drive is plotted in the white region on the right hand portion of the panel. If a plot is already displayed the user is asked whether to replace the exist- ing data. If the user decides not to replace the existing plot the latest file will be added to the display in the plot area with a different plot symbol for the data points. The symbols used for each data set can be changed - see See “Changing the Plot Appearance” on page 98. Up to eight plots can be displayed simulta- neously - after this the earliest displayed data sets will begin to be replaced. Note that the axis ranges are automatically adjusted to encompass the full range of all data sets displayed. When the .grd file is opened and the data displayed, Macro- Model will also read the structure from the corresponding .out file and display it in the main structure window.
PostScript - the PostScript button allows the user to create a file containing a PostScript representation of the currently displayed data. This can be included in a word-processing document of printed directly to a postscript-compatible printer. There are a number of options the user can set before the file is created. The Title field allows the user to enter text which will be placed above the plot. The plot
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orientation can be either portrait (8.5x11'') or landscape (11x8.5''). The actual size of the plot on the page will be approximately that of the plot displayed in the screen. If this exceed the size of a page then the image will be reduced in such a way so as to maintain the aspect ratio displayed on the screen. If the postscript file is to be included in another document the Center on Page option should be off.
Tabular Data - This button allows the creation of a file which contains the data displayed in the plot region in tab-delimited format. This file can be imported into graphing packages, spreadsheets etc. All data sets currently displayed will be written to the file.
1D Slice - If the .grd file opened by the user is from the driving of two angles then the 1D Slice button will become active. This allows the user to access a panel which is used to control how data from the 2D grid is displayed. When a 2D .grd file is read the data displayed represents a constant value of one angle and variation over the full range of the other angle. The 1D Slice button has a pair of radio buttons which allow the user to select which of the two angles is to be held constant and a slider to set the value at which that angle is to be held. Changing the value of the slider will also update the corresponding angle in the structure dis- played in the main MacroModel window. The 1D Slice is only active if the most recent data set which was read was from a two-angle drive.
Constant Angle Angle: 11-8-5-1 Angle 8-5-1-3
Angle: 0.000
Done
96 MacroModel User Manual Version 7.0 Interacting with the plot
Absolute and Relative Energy - by default the data read from the .grd file will be displayed in absolute units of kJ/mol. If the Relative Energy button is selected then the display will be changed to show the energy relative to the lowest point in the profile. This is useful for comparing profiles calculated with different forcefields or other energy options which affect the torsional energy profile.
Interacting with the plot
If the mouse is clicked in the plot region several actions occur. Firstly the angle and energy value corresponding to the current position of the mouse within the plot is reported in the text fields in the left hand portion of the panel. In conjunc- tion with the Relative Energy mode this allows the measurement of rotational energy barriers. As well as this display the structure in the main MacroModel window will have the corresponding torsion updated to reflect the position of the mouse along the X (angle) axis. The structure on the screen and the energy/angle report in the panel will remain continuously updated until the mouse button is released or the mouse pointer moves outside of the plot region.
Data Set Name:
Symbol Size: Apply size to all data sets. 3
Curve Width: Apply width to all data sets. 2
Join Points
OK Cancel
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Changing the Plot Appearance
It is possible to change the appearance of the plotted data. At the top of the plot region is a legend area which relates the data set to the plot symbol. If the mouse is clicked on a symbol in a legend area a editor panel will appear which allows some changes to be made to the way that data set is displayed. Firstly the name displayed in the legend area (which by default is the prefix of the .grd file) can be changed by entering a new entry in the Data Set Name field at the top of the panel. Directly below this is a menu which allows selection of the plot symbol for the data set. Clicking in one of these boxes will change the current selection. In addition to the symbol type, the size of the plot symbol can also be adjusted using the slider labeled Symbol Size. If the Apply size to all data sets toggle button is on then the size selected will be applied to all data sets in the plot not just the one which was used to bring up the plot appearance editor panel. Finally the width of the lines which connects the data points can be set by using the slider labeled Curve Width. Again this selection will be applied to all data sets if the Apply width to all data sets toggle button is active. To turn off the connecting line segments turn off the Join Points toggle button. Changes made in this panel will not be reflected in the Plot region until the OK button is used to dismiss the panel. If the Cancel button is used to dismiss the panel then the no changes will be made to the plot.
4.10 Structure Plotting - Plot
MacroModel can create Chem3D, PostScript and SGI IRIS RGB plot files. The Chem3D files are created using Cartesian Coordinate 2 format. Note that Chem3D Plus will now read MacroModel structure files directly.
PostScript files may either be included in documents such as MicroSoft Word or plotted directly to a PostScript printer. If included in Word, you will not see the image while editing, but it will print out. Also, there are two styles of PostScript plots -- wireframe and pixelmap.
RGB plots are only available when in 3D mode and when running on an SGI. These files can be used with many SGI applications. Also, they can be imported into Debabelizer on a Macintosh and then copied and pasted into other Macintosh applications.
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Wireframe
Postscript plots can generate either wireframe or pixelmap images. Wireframe plots are much quicker to generate and plot than the pixelmap plots. Wireframe plots may be plotted by bond order or by depth cueing. Bond order plots display bond width based on bond order. Depth-cued plots display bond widths depend- ing on the distance from the viewer. Bonds that are farther away are smaller and bond order has no effect on bond width. For both types of plots all bonds are sorted according to the z midpoint of the bond. This provides correct depth infor- mation in almost all cases. It is possible that there will be cases where an actual z- buffering algorithm would be required to give completely accurate bond overlap, but these cases will be rare.
Please note the following concerning wireframe plots. In the 3D mode of the pro- gram plotting disregards the clipping planes. All bonds are included along the z- axis while bonds outside of the viewing window are clipped. Also, wireframe plots always generate wireframe images regardless of the on-screen representa- toin. Additionally, if on-screen in either mode (2D or 3D) , the following are also plotted: the atom labels, ADist's (Angstrom distances), Bangl's (Bond Angles), Dangl's (Dihedral angles), Atom or molecule numbers. Please note that neither volumes nor surfaces are plottable. Lastly, if you wish to plot a subset of the full connection table, clip out specific atoms for plotting. This can be accomplished by using the Clip button at the top of the Main Button Panel.
PixelMap
Pixelmap plotting is available only in 3D mode and produces color PostScript files 33DD of what is on-screen in the 3D Viewing Window. As such it is What You See Is What You Get (WYSIWYG) printing. You will get exactly what appears in the Viewing Window area. The program takes a snapshot of the on-screen area that corresponds to the location and dimensions of the Viewing Window. That is, it takes a 'picture' of the pixels. Anything that is within the borders of the 3D win- dow (including the) will be printed. We recommend that you turn off the Control Window by using the Opt panel to do so. Also, note that the program pops the Viewing Window in front of all the other windows while it is taking the snaphot. If any other windows are placed within the borders of the Viewing Window before the snapshot is finished, there is the possibility of having them appear in the final output (typically as black rectangles).
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The PostScript files generated by the pixelmap method tend to be large -- around 6 megabytes of data. This is one of the reasons the files tend to take a long time to print. In fact, we recommend that you do not print these files over a serial connec- tion. We have found this to be unreliable and extremely slow. We suggest you use a faster communication channel to print (like AppleTalk). We actually transfer our files to a Macintosh and print the Pixelmap PostScript files over AppleTalk using a freeware program called maclpr. This program was written by Takahiro Sumiya of Hiroshima University, Japan. He can be reached at [email protected] or try downloading the software from one of the standard Mac freeware servers.
The larger the 3D Viewing Window is the better the final image will be. This is due to the maximum pixel size of the screen (typically 1280x1024) and the resolu- tion of the printer which is usually at least 300x300 per inch. Thus, a one to one mapping of pixels of a full-screen image to 300x300 dpi printer would generate a plot approximately 4x3 inches. The plotting facility, however, always scales the plot to fully fill the paper. Thus, the mapping to an 11x8.5 inch sheet of paper (landscape view) on a 300x300 dpi printer is approximately 1 pixel to 3 dots. If one shrinks the 3D Viewing Window in half to 640x512, the final plot will be more jagged looking since the ratio is much larger, approximately 1 to 6. In gen- eral, leaving the 3D viewing window at its original almost full-screen size will produce good quality plots on a 300x300 printer. The larger the window the smoother the final printed image; conversely, the smaller the window on-screen the more jagged, or rougher the final printed image will appear.
Other
Users may choose to send the output either to a file or direct the output to a print command. A default print command can be set-up in the $MMSITEDIR/mmod- site.dat file. Please see this file for configuration details.
Use KERMIT (available from Columbia University) or ftp (available from NCSA telnet and others) to transfer plot files to a Macintosh or other machine.
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4.11 Boolean Operations on Atom Sets - ABool
MacroModel frequently uses the concept of sets of atoms. There are four sets which are used throughout the program -- Set1, Set2, Set3, and the Working Set. These sets can be defined based upon different user-selectable criteria and provide a convenient method for grouping atoms together. These groups may then have specific operations performed on them. Some of these operations include calcu- lating volumes, recoloring of atoms, and deleting atoms to name a few.
In the past, once one or more sets had been defined the user could perform various Boolean operations (AND, OR, XOR or NOT) from within SETS mode. The Atom Sets Panel makes Boolean operations easier as well as amodal (i.e. you don't have to be in SETS mode to use it). Access the panel by selecting the ABool button in SETS mode. Once the panel is visible it can be used at any time from within MacroModel.
Atom Sets Operand 1 Operator Operand 2 Result Load From Set1 AND Load From Set1 Do & Put Into Set1 Load From Set2 OR Load From Set2 Do & Put Into Set2 Load From Set3 XOR Load From Set3 Do & Put Into Set3 Load From WorkingSet NOT Load From WorkingSet Do & Put Into WorkingSet
Help Quit
To perform a Boolean operation the user loads Operand1 and Operand2, selects a Boolean operator, and then chooses an output set (Set1, Set2, Set3 or the Working Set). The Boolean operation is performed at the time the output set is selected. Note that Operand1 and Operand2 can be loaded with the contents of either Set1, Set2, Set3 or the Working Set. Once loaded an operand will retain its values until either it is reloaded or MacroModel terminates. So, for example, it is possible to define a Working Set and load it into Operand1 and define a different Working Set and load it into Operand2.
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4.12 Volume Boolean Operations On Molecules - MBool
MacroModel provides the ability to calculate and display volumes of on-screen 33DD structures. It also allows users to calculate and display Boolean (AND, OR, NOT IN) combinations of on-screen volumes. The Volume Boolean Operations On Molecules panel (hereafter referred to as the VBOOM panel) allows users to do volume calculations on molecules. This differs from the existing MacroModel methods which require the user to choose specific sets of atoms for volume calcu- lations. Although the previous volume calculation facilities are flexible, they are sometimes difficult to use. It is hoped that the VBOOM panel will greatly sim- plify the calculation of simple, molecule-based volumes.
The VBOOM panel allows users to do the following volume calculations: pick a molecule and display its volume, pick two molecules and calculate/display some Boolean combination of their volumes.
Volume Boolean Operations On Molecules (VBOOM)
To Load Molecule: Select button. Choose a molecule. Molecule 1 Molecule 2
Molecule 1 Molecule 2
Common To Both (AND)
In Either (OR)
In Molecule 1 Not In 2
Do Operation Help Quit
To perform a Volume calculation the user first selects one or two molecules.
This is done via the two push buttons Molecule 1 and Molecule 2. For exam- ple, to load Molecule 1, one selects the Molecule 1 button and then clicks on an atom in the molecule of interest. Molecule 2 would be similarly selected.
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The next step is to select an appropriate Volume option: Molecule1, Molecule 2, AND, OR, or In Molecule1 But Not In Molecule 2. Some options require that both molecules be defined; the first two require only one. To do the actual calculation and display the volume the Do Operation button must be selected.
4.13 Ribbn (Ribbon Panel)
Use this panel to generate ribbon diagrams for proteins and peptides. The panel 33DD allows one to control the display characteristics of the ribbon. Users may choose among a number of items which include the representation and coloring scheme of the ribbon (see below). To actually generate a ribbon select the options you want from the Ribbon Panel and then click on Replot.
The Ribbon Panel provides flexibility in the viewing options. Options include the following (for a complete description see the on-line MacroModel help facility for the Ribbn button):
CAlpha Connects Alpha Carbons with a single line Trace Segmented Connects the guide points with straight lines Fitted A B-spline curve is fitted through the guide points Curve Curved A B-spline curve is fitted through the guide points and Sheet1 shaded Curved Uses a different method to create the curved shaded Sheet2 sheet Flat Sheet Shaded polygons are drawn between the guide points Table 9. Ribbon Representations
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Ribbon
Representation Options 5 Segmented Display Ribbon Fitted Curve Number of Lines Display Structure Display Perpendiculars Flat Sheet 1.0 Two-sided Lighting Lighting Panel Separation (Ang.) Color By Strand
Replot Help Quit
Note that the Ribbon Panel differs depending on the hardware configuration of your machine.
The Ribbon Panel requires that the residue sequences are sequentially numbered. You can not, for example, grow a sequence and then replace a residue in the mid- dle (if you wish to plot ribbons). A ribbon plot of such a structure will not be cor- rect. You must insure that the sequence is correctly ordered. Any necessary reordering can be done by writing the structure out as a PDB file and then by read- ing this PDB file back into MacroModel.
You must be running in the 3D GL mode to use ribbons. There currently is no rib- bon support in X Windows mode.
On SGI machines use the snapshot and showcase programs to generate PostScript output. One runs snapshot, sweeps out an area of the screen to capture, and saves this image to a file. Next run showcase and Insert an Image. You can then either print it directly from within showcase if you have printing set-up. If not, you can have showcase generate a PostScript output file which can then be sent to a PostScript printer.
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4.14 Movie
Use this button to generate and view a movie. Movies are made from BatchMin runs that have sampled the output structures. This can be done, for example, in dynamics by turning sampling on for the run. When Movie is used it first gener- ates a binary movie file from the .out file and then proceeds to use the binary file for subsequent displaying of the movie. Future invocations of Movie for a partic- ular job allow the user to either regenerate the binary movie file or if it is present use the existing movie file.
Users may choose to generate a movie which colors atoms either by atom type or by energy.
4.15 Hydrogen Bonding (Hbond, HPref Buttons)
Use the HBond button to display hydrogen bonds. The hydrogen bonds dis- played correspond to those involved in energy calculations. Either working set or all atom hydrogen bond display is permitted. The hydrogen bonds are erased when this button is turned off, or when you leave the ANLYZ mode. Note that hydrogen bonds are only displayed when explicit hydrogens are on heteroatoms and the displayed set may contain some hydrogen bonds which are not part of those considered by any particular force field. Only those bonds which are found are candidates for inclusion as hydrogen bonds in energy calculations.
Hydrogen bonds are displayed when the H and the acceptor (A) are no more than the hydrogen bonding cutoff distance apart (by default 2.5 Angstroms), when the D-H --- A angle is at least the minimum donor angle (default of 120 degrees) and when all H --- A-R angles are at least the minimum acceptor angle (default of 90 degrees). These values are the default parameters that MacroModel uses. The HPref button allows the user to set the following cutoffs: maximum distance (ini- tial value is 2.5 angstroms) minimum donor angle (initial value is 120.0 degrees) minimum acceptor angle (initial value is 90.0). Any time HBond is on the cur- rently set preferences are used to determine which hydrogen bonds are displayed.
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4.16 Photo Mode
Photo mode is used to enlarge the 3D Viewing Window to full-screen and hide the window borders. This mode can be toggled into and out of by pressing the F1 function key. This makes taking photographs of the screen better since it provides a single solid colored background. This facility is only available in the 3D GL version of MacroModel.
4.17 ASL (Atom Specification Language) Panel
The ASL Panel is located in the SETS mode of ANLYZ. Once the panel has been activated it can be used from anywhere within MacroModel. Ultimately this panel will be further enhanced and will replace the current SETS submode.
This panel allows users to specify sets of atoms via a command language. It allows sets to be defined by a number of different criteria. These include but are not limited to: atom type, atom number, residue type, residue number, molecule number, distance. Selected atoms are immediately placed in the working set over- writing whatever may be there. To see which atoms have been selected the Mark option in SETS, SURF or DISPL must be turned on.
The Buttons
The ASL panel also has four buttons located in its bottom part. These buttons are ENTER, OPEN, SAVE AS.., and QUIT. The Enter button has the same effect as a press of the return key when entering commands. The Open button permits opening of any file containing several ASL commands that were previously saved. If a file is opened while some commands are present in the ASL command list, the commands in the file will be appended to the commands currently displayed. The Save As button will create a .asl file which holds all the commands that are pres- ently in the window. The Quit button will unmap the ASL panel.
Commands (classes) and Properties
The command language uses PDB names/types as the default. To use the Macro- Model names/types you must append .mtype to the commands (See below). Note that abbreviations for commands and their properties are provided (see below).
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(m)olecule. number# Molecule number (c)hain. name# Chain name (r)esidue. (pt)ype# PDB residue type (mt)ype# MacroModel one-letter residue code (n)umber# Residue number (p)olarity # Polarity (h)ydrophobic # hydrophobic residues (pol)ar# polar residues (pos)itive# residues with a formal positive charge (n)egative# residues with a formal negative charge
(a)tom. (pt)ype# PDB atom types (n)umber# Atom number (mt)ype# MacroModel atom type (e)lement# Element symbol for the atom (p)olarity# Polarity (a)ttachments# Number of bonds the atom has (c)harge# Partial charge
Operators and (Boolean and) or (Boolean or) not (Boolean not) fillres(fill residue) fillmol(fill molecule) within(select all atoms that are N angstroms or less away) beyond(select all atoms that are further than N ang- stroms)
Operator Priority (decreasing priority)
not/fillres/fillmol and/or within/beyond
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Full Descriptions of Commands
The command syntax is of the form: class.property propertylist where a complete specification is a class name and some property specified by a property name and property list. All names of properties and characters in property lists will be treated in a case insensitive manner.
Wildcards will be supported for atom and set names. A "*" will match zero or more characters and a "?" will match any single character.
Comments can be included in the specification - any text after a "#" character will be ignored.
Items in a property list may be separated by comma, whitespace or both. Ranges (lower-upper) may be used where appropriate. Unterminated ranges are taken to include all available numbers. For example if there are four molecules in the sys- tem then the following specifications are identical:
mol. >1 mol. >=2 mol. 2-4 mol. 2, 3, 4
The parenthesized character(s) represent the minimal characters that must be typed in for the command to be recognized. Note that all commands end with a '.'. So, for example, it is acceptable to enter: 'm.' for the molecule command. Com- mands differ from aliases which are not as flexible but can be configured as short cuts (see below). (m)olecule. This is the top level class in the language. The term molecule is used in the normal chemical sense meaning all atoms which are connected by a single covalent path.
(c)hain. This corresponds to a chain as specified in the PDB file format. Note that this chain may be a subset of a molecule (e.g. when chains a linked by disul- phide linkages)
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(r)esidue. An arbitrary collection of one or more covalently bound atoms within a molecule, such as the monomer units in a polymer.
(a)tom. A single atom.
Abbreviations/Aliases
Abbreviations are listed in the $MMSITEDIR/alias.def file. These are also known as aliases. Aliases differ from commands in that the exact (case sensitive) string must be used when using an alias. A command on the other hand may use any set of characters as long as they minimally define the command. See the com- mands above. The parenthesized characters define a minimal definition for that command. Again, note that commands end with a '.' while alias do not require one (since they're aliases).
You may add aliases to the $MMSITEDIR/alias.def file.
Some Examples
res. ala 1 2 3
will return atoms which are either in residues 1,2 or 3 or are alanines (so if res 4 is an alanine it gets included).
res.type gly,val,ala res. gly val ala
are equivalent. Return all glys, all vals plus all alas.
residue. 1-4 residue.number 1,2,3,4 residue. 1,2,3,4
MacroModel User Manual Version 7.0 109 CHAPTER 4: Analyze Mode
are equivalent. Returns atoms in residues 1 through 4.
atom.charge 0.400# Atoms with charge equal to 0.4 atom.charge -0.6--0.4# atoms with charges -0.6 to -0.4 atom.charge <0.0# atoms with neg. partial charges atom.charge >=0.5# atoms with charges >= 0.5
mol. 1 and atom. CA # all the alpha carbons of molecule 1. res.num 1-100 and res. ala# all alanines in the residues # with numbers in the range 1-100
These are boolean operations. So 'and' means that for an atom to be accepted it must pass both of the criteria ('or' simply must pass either criteria).
Notes
See the $MMOD_ROOT/doc/atomspec.doc file for more details as well as a further description of the atom specification language.
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CHAPTER 5 Other Programs
This chapter describes other programs that are included in the MacroModel distri- bution. Some of these are accessible via the SYSTEM button in the Main But- ton Panel of MacroModel. Others can be started up via scripts located in $MMOD_ROOT.
5.1 Xrbm
Overview
Xrbm is a graphical user interface for controlling and submitting remote Batch- Min jobs. Just as rbm (Remote BatchMin) provides network transparent Batch- Min job control without starting MacroModel so too does xrbm. While it makes the bookkeeping and process of controlling and monitoring remote serial Batch- Min jobs easier, it is not an interface for running distributed BatchMin jobs. This should be done by configuring a command file with distributed BatchMin com- mands and then by running a master BatchMin.
Running xrbm
xrbm is located in the $MMOD_ROOT/run/exec directory, but should be run from $MMOD_ROOT just typing xrbm. It can also be accessed via the SYSTEM but- ton in the bottom of the Main Button Panel of MacroModel.
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In order to run BatchMin jobs using xrbm one needs to have the BatchMin Net- work Server correctly installed. This means the BatchMin Network Server (i.e. the BatchMin deamon, bminrd) must be installed. See “BatchMin Network Server Installation Instructions” on page 134 for installation instructions.
When started from a specific directory xrbm will automatically check for all the runnable jobs in that directory and post their name on the first scrolling list of the interface. A runnable job is composed of two files with the same base name and different extensions, one .dat for one file and a .com extension for the second file. For example, mmodtmp will be posted in the first window if mmodtmp.com and mmodtmp.dat are present in the working directory. Also at start-up all jobs that were started and that are still running, sleeping or halted will be posted in xrbm with their current state. The two above described windows are mutually exclusive, meaning that a job that appears in the first window cannot appear in the second one because it has not been started yet. Once it is started it is removed from the first window and posted in the second. To start a job one should select its name from the first window by a mouse click. The run button will enable and some default values for the hostname, username and the version of the BatchMin to be run are posted in text fields and can be changed by the user as needed. When all the information in those text fields are set click on the start button to run the job.
Monitoring a BatchMin job
Once a job is started it can be monitored using the buttons in the lower level of the xrbm window. Any job to be monitored needs to be first selected from the second window. At that point the buttons info, halt, get, sleep, wake and update should be active and would do the appropriate action.
Button Descriptions
For any of these buttons first select the job from the appropriate list and then select the button.
INFO: This button will write information about the selected job in the Output window. Display the Output window by clicking on the Output toggle button.
RUN: This button will start up the job that is selected
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HALT: This button will stop a running job. The job will be listed as completed.
GET: This button is used after a job is completed. It will copy all the files from the remote host to the local host. You may also use it while the job is running to retrieve automatically all files associated with the job.
SLEEP: This button will put a running job into a suspended state, which is equiv- alent to a pause. The job will not use any CPU, but it will continue to hold onto other resources that it had been using like swap. The only valid command after putting a job to sleep is to wake it up.
WAKE: This button is applied on a sleeping job. It will restore it to the running state. At this point other actions can be taken on this job. Waking up an already running job has no affect.
UPDATE: This button is used to request an immediate update of the state of BatchMin. The BatchMin output files are immediately updated with the latest information. This is written toa number of files including the .m1 and .m2 files.
Troubleshooting
You get "dat file specification not correct". The first two lines of a command file must contain a local file name. So, /usr/people/mary/ in1.dat is not acceptable and must be changed to in1.dat. The same is true for the output file name.
If you experience problems with xrbm, then it is possible it is a problem with the rbm/bminrd (BatchMin Network Server) configuration. If this happens, please use the “Trouble Shooting” on page 141
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APPENDIX 1 Installing MacroModel
1.1 MacroModel Directory Structure
The top-most directory where MacroModel was loaded is referred to as $MMOD_ROOT. $MMOD_ROOT contains two subdirectories, run and src. The run subdirectory is divided into exec and mmdat subdirectories. exec contains all executable files for MacroModel, BatchMin, XCluster and associated utility programs. mmdat contains data files used by MacroModel and BatchMin. The src directory (if you have a source copy of MacroModel) contains mmod (Mac- roModel source) bmin (BatchMin source) subdirectories, and xcluster (XCluster source) directories.
Environment Variables
The environment variable $MMOD_ROOT needs to be set to the directory where MacroModel was loaded. When the macromodel shell script is executed the environment variable $MMOD_ROOT is set to the current working directory by default. You may set $MMOD_ROOT to a particular directory by setting the $MMOD_ROOT environment variable. This will allow you to start up MacroModel from locations other than the directory where it was originally loaded.
$MMSITEDIR and $MMEXECDIR are environment variables that MacroModel also uses. $MMSITEDIR is the default location for the mmodsite.dat file, fragment files, force field files, solvent files, hostfiles.dat file, and any shell scripts referenced in hostfiles.dat. MacroModel first searches locally for
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these files. If one is not found, MacroModel will search for it in $MMSITEDIR. This allows a user to access system wide defaults in the $MMSITEDIR directory or override a file (or files) by placing a file (or files) in the local directory. $MMEXECDIR is the location of MacroModel, BatchMin and other executable images.
INClude directory paths
There is one include directory, INC1. This will default to $MMSITEDIR. The default value can be superseded by setting INC1 paths in mmodsite.dat. INC1 specifies the location of fragment template files, button help file (mmt- plx.doc), and volume initialization files.
Silicon Graphics Installation
A description of the installation instructions also appears in the MacroModel User's Manual in Appendix 1 Installing MacroModel
The X window server must be installed to run MacroModel. Insure that this is done by entering the commands
setenv DISPLAY
where
1. 1. Load the distribution with the tar command :
CD-ROM:
tar xvf /CDROM/
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Where
Note: CD-ROM drives are monitored automatically and mounted on /CDROM (for the first CD-ROM drive) when a CD containing a valid file system is inserted. If the CD-ROM drive is not mounted consult your “IRIX Administra- tion Guide” for information on mounting the device on your system. Please con- tact the MacroModel Development Group if you still have problems.
Tape:
tar xvmo
2. Set environment variables:
setenv MMOD_ROOT
(where
alias macromodel '$MMOD_ROOT/macromodel'
You will need to input the above two lines every time you log in to your worksta- tion unless the lines above are put into your .cshrc file (in your home directory).
3. Run the program :
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macromodel
If energetic calculations using BatchMin are to be run on a remote computer, see “Setting Up MacroModel and BatchMin Communication” on page 125
IBM RS/6000 Installation
A description of the installation instructions also appears in the MacroModel User's Manual in Appendix 1 Installing MacroModel
The X window server must be installed to run MacroModel. Insure that this is done by entering the commands
DISPLAY=
where
1. 1. Load the distribution with the tar command :
CD-ROM:
tar xvf /cdrom/
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Where
Note: If the CD-ROM drive is not mounted please try the following command:
mount -o ro -v cdrfs /dev/
*Please note that there is a space between
If you are still having problems please contact the IBM technical support.
Tape:
tar xvm
2. Set environment variables:
MMOD_ROOT=
(where
alias macromodel="$MMOD_ROOT/macromodel"
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You will need to input the above two lines every time you log in to your worksta- tion unless the lines above are put into your .profile file (in your home directory).
3. Run the program:
macromodel
If energetic calculations using BatchMin are to be run on a remote computer, see “Setting Up MacroModel and BatchMin Communication” on page 125
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APPENDIX 2 MacroModel on a Macintosh or PC
MacroModel may be run on a Macintosh or PC using the X-Windows Macro- Model option (selection 1 on the MacroModel start-up menu). To enable your Macintosh or PC to run under the X-Windows option, the Macintosh or PC must be turned into an X-Server (an X-terminal). There are many software packages available for purchase that will do this. Please note that the information here is not intended as an endorsement. We only include the information as we are famil- iar with the products or have information concerning these products.
2.1 Macintosh
We are aware of two software packages that will turn your Macintosh into an X- Server. One is from Apple and is called MacX. The other is from White Pine Software and is called eXodus. Typical installation involves installing a commu- nications program and then the X-Server software. Usually the communications package will be MacTCP. Setting up a network connection and installing MacX is nontrivial so you will likely need help from someone with a working knowledge of networking systems.
Your Macintosh will need to be networked to a host computer since it must com- municate with the host machine where MacroModel actually runs. This Macin- tosh/host connection may be set up in several ways. The first and most desirable approach is to install an Ethernet card and connect the Macintosh directly to your host computer via Ethernet running tcp/ip. The other option is to make the con- nection via a LocalTalk network running AppleTalk. The LocalTalk network must
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be connected to an Ethernet network (running tcp/ip) to which your host machine is also connected. The LocalTalk/ethernet connection is made using a gateway box which will interface the two networks. We know of two companies that make such gateway boxes. One company, Cayman Systems, Inc., manufactures a prod- uct called a GatorBox. The other company, Shiva, produces a product called a FastPath gateway (information as of 1992).
Note that AppleTalk networks have a much smaller bandwidth than Ethernet net- works. Consequently, Macintosh X-Servers running over AppleTalk networks that are heavily loaded will run noticeably more slowly than those directly con- nected to an Ethernet network. Also, if files are to be transferred between your Macintosh and other machines on the network frequently or the files transferred across the network are large, a direct connection to Ethernet will reduce transfer times significantly.
Using MacX
Once you have connected your Mac to the network and have installed the appro- priate software your Macintosh is ready to be used as an X-Server. You should also have installed MacroModel on your SGI or IBM. If you did not, please fol- low the installation instructions in APPENDIX 1 on page 115 before proceeding.
1. Start up MacX and then get an xterm running. Doing this will log you on to the host machine creating an window (an xterm) on your Macintosh.
2. In MacX choose the menu option entitled Window Preferences... under the Edit option. Set the window style to be Simple.
3. Make sure the environment variable $MMOD_ROOT is set to the directory where MacroModel was loaded. In this case we will assume that $MMOD_ROOT is /usr/people/mmod. Please note that your value for $MMOD_ROOT may differ.
4. Run the start-up script located in $MMOD_ROOT by typing:
$MMOD_ROOT/macXmodel
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or by typing the equivalent:
/usr/people/mmod/macXmodel
Please note the capital 'X' in macXmodel
5. Since a Mac has only a 1-button mouse, MacX simulates a 3-button mouse as follows:
To Get Take Following Action Left mouse button Middle mouse button + left arrow key Right mouse button + right arrow key Table 11. Mac Emulation of 3 Button Mouse
Product Company Telephone Number MacX Apple 800-776-2333 FastPath Shiva 800-458-3550 GatorBox Cayman Systems, Inc. 800-473-4776 or 617-494-1999 X-Window System O’Reilly & Associates, Inc. 800-338-NUTS User’s Guide Table 12. Macintosh X-Server and Network Products
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2.2 PC
There are many packages that will turn your PC into an X-Server. One is from VisionWare and is called XVision and we have used this here. Typical installation under Windows involves installing a communications program (typically bought from a different company) and then the X-Server software. For networking we have used software from FTP Software, Inc. to give us tcp/ip connectivity. Once your system has networking software installed (this is usually tcp/ip-based but can also be DECNET-based depending on your needs and the requirements of the X Server package you purchase), then you need only install the X Server package. Setting up a network connection and installing an X Server package is non-trivial so you will likely need help from someone with a working knowledge of network- ing systems.
Your PC will need to be networked to a host computer since it must communicate with the host machine where MacroModel actually runs. This PC/host connection may be set up in several ways. The most desirable approach is to install an Ether- net card and connect the PC to your host computer via Ethernet running tcp/ip.
Just as with the Macintosh most PCs do not provide a three-button mouse. Unlike the Macintosh, however, some do come with two-button mice. MacroModel uses a three button mouse which can be simulated with either a one- or two-button mouse. Since the number of buttons varies depending on the exact mouse that one has and the method of simulating a three-button mouse (if necessary) vary, you will need to read the documentation that comes with your X Server package. The important thing to remember as far as MacroModel is concerned is that picking is done with the left button (button 1), transformations are done with the middle but- ton (button 2), and the help facility is invoked by clicking the right mouse button (button 3) over any of the Main Button Panel buttons.
One last note. We have found that performance varies depending on the resolution that is being used on the PC display. Lower resolutions can increase performance dramatically. Thus, if rotations and/or translations feel slow, try setting the resolu- tion to a lower setting, restarting your X Server, and rerunning MacroModel.
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APPENDIX 3 Setting Up MacroModel and BatchMin Communication
3.1 Summary
MacroModel - BatchMin communication is typically done through the file sys- tem. If BatchMin is run on the local computer (i.e. the same computer that Mac- roModel is running on), typically no changes to the default installation are required. In some cases users may need to add or modify the default installation to allow for, say, interaction with a queuing system or additional executoin of commands before or after a job is run. In this case additional entries need to be added to the hostfiles.dat file which is located in $MMOD_ROOT/run/ mmdat (i.e. the $MMSITEDIR directory).
If BatchMin is run on a remote computer (i.e. not the computer where Macro- Model is running), then one of two methods may be used to set up a connection to the remote BatchMin. The first method (we will refer to this as NFS-style) requires the remote machine NFS mount the local file system. The other method (called the server method) involves installing the BatchMin Network Server.
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3.2 How To Install Entries In hostfiles.dat
Each entry in the hostfiles.dat file consists of two lines. The first line is the name of a script file or the name of a host. The second line (which MUST be included) contains either nothing, a directory name, or a ’*’ followed by an optional program name. When creating a n entry for jobs which are to be run locally an entry will consist of the name of the script in the first line (which will be used to run the job)and nothing in the second line. When creating an entry for NFS-style remote jobs (see below) the first line will containt the name of the script and the second line will contain a directory. When creating an entry for remote server jobs the first line will contain the name of the host where jobs are to be run and the second line will contain a ’*’, which may or may not have after it the name of the BatchMin executable to run. If there is no name, a default is used.
Everytime a user clicks on the Host button in MacroModel it first looks in the local directory for a hostfiles.dat file and if it finds one it uses it. Other- wise it looks in the $MMSITEDIR directory for hostfiles.dat.
3.3 Adding Entries For Locally Executing Jobs Entries for jobs that are to be run locally can be added as follows. First, create a script that can be used to start up BatchMin. For examples look in the $MMSITE- DIR directory. One such file is the bmin1K script. Note that MacroModel always passes the base name of the job to a script.
Once you have created a script file test it out on the command line (from the UNIX prompt) to make sure that it can be used to run a BatchMin job. If it is not working, make sure to check that:
• the script has sufficient execute permissions • that it is handling the name it was passed correctly (the script should be run using a syntax like: myscript
To add a working script edit the file hostfiles.dat. Choose a location in the file (note that putting the entry in the first position will make it the default). Add the name of the script on the first line and an empty line as the seond line.
126 MacroModel User Manual Version 7.0 Troubleshooting
In MacroModel click on the Host button and you should get a scrolling list that includes your new entry. Select your entry. You should not get any error mes- sages or warnings. If you do, reedit the hostfiles.dat file and look for and fix any errors. If there are no errors, then try to start up a job.
Troubleshooting
Symptoms
If you are getting the following in the Message Window:
Submitting BatchMin job Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Waiting For First Intermediate Structure Batchmin Job Not Confirmed Checking .log File ...... log File Open Failed.
This almost always means that the job failed to start. Possible reasons are:
• the script you created did not have execute permissions • the script you created did not start up BatchMin properly (check path, name, etc.) • the script you created started up BatchMin in such a way that BatchMin did NOT write its output files to the current directory • the entry in the hostfiles.dat file is incorrect - you did not put in two lines for the entry (with the second empty), misspelled the name of the script, etc.
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Actions
If you did get a log file (i.e. you did NOT get the above ' .log File Open Failed.' message, then check it for further information by clicking on ComFl and choos- ing 'Display BatchMin .log Output File'. If there is no .log file or no further infor- mation in it, check and fix any of the above listed symptoms. On an SGI if you get the mssage 'killed' in the log file, then you will need to enable virtual (logical) swap space. Read $MMOD_ROOT/doc/swap.doc which is on-line.
3.4 NFS Style Remote BatchMin Installation Instructions
How the NFS Style Remote BatchMin Facility Works
How to install entries in hostfiles.dat
Create Start-up Shell Script Files
1. Insure that rsh is installed and operating correctly.If MacroModel is running on computer local_iris and BatchMin is to run on computer remote_iris then test rsh with
rsh remote_iris -l
This command will print a listing of the contents of the home directory for user
2.Create a shell script of the following form:
#!/bin/csh -f rsh remote_iris -l
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(
Note: this shell script can be tailored to the local environment as necessary.
When MacroModel executes this shell script the name of the command file will be passed as the first parameter. If the above shell script were named run_batchmin and the BatchMin job named peptid_1, MacroModel would execute:
run_batchmin peptid_1
Use this command to start a BatchMin job and test the shell script.
3.Put the shell script in the local directory or in $MMSITEDIR
4.Use the name of the shell script as the first line of an entry in host- files.dat.
Establishing a shared directory with NFS
The second line of each hostfiles.dat entry associates a mount point with each start-up shell script. In some cases this entry is left blank. When starting BatchMin, MacroModel concatenates the hostfiles.dat mount point entry with the current working directory (i.e. the directory where MacroModel is exe- cuting) to create a directory path. This path is put in the first line of the BatchMin command file, and represents the remote computer's link to the local directory where MacroModel executes. The files that MacroModel and BatchMin use to communicate are created in this directory.
There are two ways to mount the remote file system: (assume two computers - local_iris and remote_iris)
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1. The remote_iris mounts the local_iris file system Use this method if Batch- Min files should be created on the computer is executing MacroModel.
2. The local_iris mounts the remote_iris file system Use this method if Batch- Min files should be created on the computer that is executing BatchMin.
Case 1
The remote_iris computer has remotely mounted the local_iris computer file sys- tem. (the file system must be exported with write privileges).
Suppose local_iris has a file system
/usr
and that remote_iris mounts this file system as
/local_iris
Create a soft link on remote_iris as follows:
mkdir /iris_link ln -s /local_iris /iris_link/usr
In hostfiles.dat the corresponding entry is:
remote_bmin_startup_script
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/iris_link
Suppose a user runs MacroModel on local_iris from the directory /usr/peo- ple/chemist
On starting BatchMin, MacroModel will concatenate the mount point entry and the current working directory to create /iris_link/usr/people/chem- ist
This path will be put into the BatchMin command file on the first line.It will be the case that:
/iris_link/usr/people/chemist
is the same as
/local_iris/people/chemist
on remote_iris; which is the same as
/usr/people/chemist
on local_iris. MacroModel and BatchMin will communicate through this direc- tory.
A single hostfiles.dat entry and start-up shell script can be used by any user in
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/usr
on local_iris.
Case 2
The local_iris computer has remotely mounted the remote_iris' computer file sys- tem. The file system must be exported with write privileges.
Suppose there is a file system on remote_iris
/usr
and this file system is mounted remotely by local_iris as
/remote_iris
Create a soft link on remote_iris
ln -s /usr /remote_iris
Leave the hostfiles.dat mount point entry blank. MacroModel can now execute on local_iris from the remote file system
/remote_iris
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and BatchMin files will be created on the remote_iris file system.
Notes
1} In both cases MacroModel executes on local_iris. In case 1 on a local file system, in case 2 on a remotely mounted file system. In both cases BatchMin is started by executing a rsh command.
2} In both cases a single hostfiles.dat entry and BatchMin account on the remote_iris can be shared by multiple users. The force field files can be given read only protections and access to the account can be controlled with the .rhosts mechanism.
3} Soft links can be avoided by using the following naming conventions when mounting remote file systems:
If the local file system is
/usr
name the remote file system
/local_iris/usr
( i.e.: remote_iris remotely mounts the local_iris file sytem /usr as: /local_iris/usr)
Use /local_iris as the mount point entry in hostfiles.dat.
4} Do not make files with following names:
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*.m1 *.m2 *.out *.lck *.com *.dat *.log *.stp *.upt *.slp *.mmo *.grd mmodtmp.*
Read section 3.8 on page 145 at the end of this appendix.
3.5 BatchMin Network Server Installation Instructions
Overview
The client-server works as follows. The client initiates contact with inetd, the internet super server, on the remote machine. bminrd, the BatchMin remote dae- mon, is then started by inetd. Once bminrd has been started the client can send a request to the bminrd daemon (server). This can be thought of as a remote proce- dure call (similar to a procedure or function call in a program, but a request to do this is actually sent to a remote machine). The procedure executes and then a reply indicating the return status of the procedure call is sent from the server to the client. Additional information may also be passed back and forth during a request and/or during a reply. This mechanism of making requests and getting replies is how the BatchMin Network Server accomplishes its tasks, which include starting jobs, inquiring about the status of jobs, and retrieving the output of jobs.
Prior to 5.0 the underlying mechanism was socket-based. As of 5.0 RPC is used. RPC stands for Remote Procedure Call, a high-level communications paradigm which allows programmers to develop network applications while hiding many of the details of the underlying networking mechanism. It is used in many applica- tions, among them NFS.
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Installation
If a non-NFS based, network connection to a remote BatchMin server is desired, execute the following instructions. For each host that you wish to run BatchMin jobs on, the procedure outlined below must be followed.
•1)Load the distribution tape onto the machine that will run BatchMin. •2)Log in as superuser (root). •3)Follow the directions below for your computer architecture:
The information that needs to be entered below should contain the values as they are listed here. Exceptions are noted. Be aware that use of '\' means continuation of a line. Do not start a second line when entering this information as it will NOT work.
Conventions
Square brackets denote optional arguments that may be specified or not.
[debug] If present, bminrd spits out copious output to the syslog file. On SGI's this file is typically in /var/adm/SYSLOG (note the capital letters) while on IBM's syslogd must be told to dump information to a file of your choosing since by default syslogd does not write to a file (so you will get nothing!).
Angled brackets indicate that everything in between including the brackets should be replaced:
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Step1: Informing inetd
First, inform inetd about bminrd (i.e. register the bminrd program with the port- mapper). The following files must be edited: /etc/inetd.conf, /etc/ rpc. Then some system commands are executed. Two sections follow -- one specifc to SGI workstations, one specific to IBM workstations. Other platforms have similar formats to their inetd.conf files.
SGI INSTRUCTIONS
On an SGI add the following information to the following files. To /etc/rpc add:
bminrd 630474513
To /etc/inetd.conf add:
bminrd/1 stream rpc/tcp wait root
The [debug] option may be included (without []) or not added. If used, it sends copious output to the system log, SYSLOG. Only run in debug mode when trying to debug a problem. The following must be done to the system as root after edit- ing the above files. Send the hangup signal to the super-server:
/etc/killall -HUP inetd
Then make sure that the daemon is registered by making sure that
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rpcinfo -p
returns a line for bminrd that looks exactly like following except possibly for the port number (fourth column):
630474513 1 tcp 970 bminrd
IBM INSTRUCTIONS
There are some (annoying) limitations in the file format for the inetd.conf file on IBM AIX systems. First, there is a limit of five arguments that a daemon can accept from inetd. This means that the optional [debug] option format can not be used. To still allow debug and non-debug modes, we resort to using bminrd or bminrd_debug as the name of the process (first argument to the daemon, argv[1]).
The second limitation is that the total number of characters for all the arguments is 50. This means that using long path names for
First, make sure you are root and do
ln -s
where
bminrd sunrpc_tcp tcp wait root
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where
bminrd 630474513 bminrd
Get the process id of the inetd process by doing:
ps -ef | grep inetd
Now tell it to reinitialize itself (send the hangup signal to it):
/etc/kill -HUP
where
rpcinfo -p
This should return a line for bminrd that looks exactly like the following except possibly for the port number (fourth column):
630474513 1 tcp 970 bminrd
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Step 2: Get rsh running
First, make sure that you have rsh working to the remote account you want to use. Entries in the .rhosts file (for bminrd) require the machine name to be the same as the one returned by the hostname command. Let us assume you are logged on to a machine called chem1.chem.company.com and want to run a job on the remote host remote.chem.company.com. You must give the user, say, joe on machine chem1.chem.company.com, access to the account on the machine remote.chem.company.com. This is done via the .rhosts file in the user's account on the remote machine. See the man pages on rsh and rhosts for more details.
The host name used in the .rhosts file must be the same name as that returned by the hostname command. Thus, if one runs hostname on the local host, chem1.chem.company.com and it returns "chem1", then use this in the .rhosts file on the remote machine. If on the other hand it returns chem1.chem.company.com, then use this. In these two cases your .rho- sts entry would be "chem1 joe" or "chem1.chem.company.com joe", respectively. It is ok to have both entries in your .rhosts.
Step 3: Try Out rbm and ’jump start’ the daemon
rbm stands for Remote BatchMin and is the user interface for remote BatchMin jobs. The format of the command is:
rbm
Do the following: rbm
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Replace the <> paremeters with the appropriate values. Note mmodtmp is the name of the job which will not exist, and that the rbm program resides in $MMOD_ROOT/run/exec. You will either need to add this directory to your PATH or invoke it with the full path name. Since this is the first time an rbm com- mand is being run on the system, run the command, wait a few seconds and then interrupt it by hitting control-C (^-c). You should now be able to run rbm com- mands normally since the server is initialized.
Rerun the same command. You should get back something like:
executable : bmin remote host : chem1 remote login : joe job name : mmodtmp status : Not running (Nei- ther process nor .log exist)
If you get this, you have started the remote daemon and are now ready to use the BatchMin Network Server. You can now submit, monitor and control jobs using rbm. Also, you can use Distributed BatchMin to run certain types of simulations on more than one computer. This provides a level of coarse-grain parallelism which can greatly speed up the run time. For information on distributed Batch- Min see Appendix 4 of the BatchMin Reference Manual.
If you wish to further configure things so that jobs can be run from within the graphical user interface (MacroModel), follow the next step.
Step 4 (Optional): MacroModel -- Accessing the Server From the Graphical User Interface
You can run remote jobs from the front-end. MacroModel reads host information out of the hostfiles.dat file. Each entry is two lines. For a RPC-based server entry add the following two line entry to the hostfiles.dat file in $MMOD_ROOT/run/mmdat/:
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The first line is the hostname of the machine on which you wish to run BatchMin. The second line consists of a '*', which can be followed optionally by an execut- able name. If none is given, then 'bmin' is assumed. If one had an IBM Power2 on which he wanted to run BatchMin, the second line could be '*bmin1K- pwr2'. This would allow the user to start up a Power2 executable on the IBM. The remote host can now be chosen in MacroModel from the menu in the same fashion as NFS-based remote host entries and/or local host entries can be chosen (using the Host button in ENRGY submode).
Some Final Notes
First, either put the executable directory into the path of all users or make an alias. We use an alias. In fact, if you are only going to be using one BatchMin execut- able, then you can alias it as follows:
alias rbmin '$MMOD_ROOT/run/exec/rbm bmin'
or if you want the flexibility to choose which BatchMin do just:
alias rbmin '$MMOD_ROOT/run/exec/rbm'
In this latter case, the user will have to specify which executable they want to use. This may be desirable when a user wishes to, say, run a mips2 specific executable on a host that can do so, taking advantage of the increased performance. So in this case they might specify executable as 'bmin2K-mips2', depending on the size BatchMin she requires.
Trouble Shooting
Can Not Connect To bminrd Server or rbm Command Seems To Hang
Check to see if the daemon has been started. This can be done by doing:
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ps -ef |grep bminrd
You should see one bminrd process and it should be owned by root. If it is not running, make sure that your entries in the inetd.conf file are spelled correctly, are valid file names/directories, and have the correct permissions. If any of these are wrong, go back and repeat the steps from Step 1 on. If the inetd.conf file is correct, try to get bminrd running by reissuing the rbm command. If that does not work, then also try redoing the installation steps starting from Step 1.
Server Is Running But rbm Is Not Working Correctly
If you have problems, then there are two debug modes which may help. The first and simplest is invoked on the client side, through the rbm command. Just add the word debug to the end of the command. This will inform you of what rbm is try- ing to do and what it has or has not succeeded in doing.
If more information is required, then bminrd can be restarted to generate debug output to the SYSLOG file. This can be done by editing the inetd.conf file as described in step Step 1 and reinitializing inetd. If bminrd is not running, then fol- low the above directions in Step 3 for 'jump starting' bminrd. If bminrd is already running, then determine the process id of bminrd and execute:
kill
After a while (possibly up to 15 or so seconds) a bminrd process with a different process id should appear and the original one should disappear. If the original one disappears, but no new one is started, then use the method of Step 3 to 'jump start' the daemon. If the debug daemon starts correctly you will get output to the SYS- LOG file. On an SGI this will happen automatically and the file is typically in / var/adm/SYSLOG. On an IBM you must tell the syslogd (the syslog daemon) to send this information to some file. Do a man on syslogd. Also, there is a file, /etc/syslog.conf, which has further information on initializing system log- ging.
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Please be aware that in debug mode copious output is generated. The SYSLOG file can grow to be very large. Once debugging is no longer needed, restart the daemon in a non-debug mode.
3.6 Using the RPC Network Connection to Run BatchMin Manually
If the BatchMin RPC-based daemon has been installed, a command line interface - rbm , which prior to 5.0 was called rbmin, provides network transparent Batch- Min job control without starting MacroModel. rbm is located in $MMOD_ROOT/ run/exec/. It is executed with the following arguments:
rbm
Items surrounded by < > are required. You also must choose one of the arguments from the list at the end of the line surrounded by <>.
The
After these arguments are specified, choose the action desired: run to start a job; info to query the status of jobs; halt to stop a job; sleep to put a job to sleep; wake to restart a sleeping job, or update to force an update of a job. For instance:
rbm bmin chem1 joe job1 run
will start a job "job1" on the computer "chem1" under the login "joe"
Wild cards can be specified with the "-". For instance:
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rbm bmin - - - info
will return the status of all your jobs on the network that you started from your current login id.
An rbm command with wild cards can be executed by crontab to start or stop jobs at specific times during the day.
Read the BatchMin Force Field and Solvent Files in section 3.8 on page 145.
3.7 Installing Additional BatchMin Network Server Services
Prior to version 5.0 users installed a service that corresponded to the BatchMin executable that they wanted to run. Typically, the default installation would run an executable called bmin. If a user wanted to run a different executable, say, bmin5K750 she would have to install an additional service. In fact, for each dif- ferent BatchMin executable that one wanted to run an additional service needed to be installed.
As of 5.0 and with the advent of the RPC-based BatchMin Network Server, this is no longer necessary. Any BatchMin executable that resides in the
rbm bmin5K750-mips2 remote.chem.company.com joe job1 run
For those who installed the pre 5.0 server, we recommend that the entries for this be removed from the /etc/services and /etc/inetd.conf files.
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3.8 BatchMin Force Field, Solvent and atom.typ Files
BatchMin is organized to allow both user-modified and standard default force field and solvent files to be accessed easily. BatchMin will first search for force field and solvent files in the directory where it finds the MacroModel structure file (i.e. the directory path on the first line of the command file). We will refer to this as the local directory or the local files (even though this might not be local if for example the first line in the .com file were /usr/you/est/input.dat but you were actually in /usr/you. Typically, however, it will be the same direc- tory -- since there will be just a filename without a path in this first line). If unsuc- cessful, BatchMin will access the environment variable $BATCH_ROOT and look for the force field and solvent files there.
A user can put modified force field or solvent files in the local directory from which MacroModel or BatchMin is to be executed. These user force field and/or solvent files will be used when BatchMin is run. If one wishes to use the standard default files, then the environment variable $BATCH_ROOT should be set to the directory path where these default files are located. The default area is typically $MMSITEDIR (which is typically set to $MMOD_ROOT/run/mmdat where $MMSITEDIR and $MMOD_ROOT are environment variables). Also, users who wish to use the default files should make sure that there are no local force field or solvent files as these will override the files in the default location.
In the local directory, a file can be given either the default name (e.g. amber.fld) or else be named after the input file name (e.g job.amber, job.water, etc.). Files named after the input file have a higher priority than those with the default names.
When executing remote jobs via the BatchMin Network Server, bminrd, the order in which BatchMin will use the files are as follows. If local files are present on the local machine, they will be shipped over to the remote host and used for that job. Note you can run more than one job on the remote host and if each has its own dif- ferent set of local files then these will be shipped over to the remote host and used only for that specific job. Thus, users can have multiple remote jobs running simultaneously each with its own copy of local (i.e. user-modified) files.
If no local files are present and if BATCH_ROOT is defined in the account on the remote host, this is the location BatchMin will look for the default files. If BATCH_ROOT is not defined, then BatchMin will look in
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The same conventions hold for the atom.typ file.
3.9 Configuring bminrd, the BatchMin Network Server, to Start Automatically at Boot Time on an SGI On SGI machines the BatchMin Network Server can be configured to start up automatically at boot time. Note that the server must still be installed as described above.
To configure automatic start-up a template script is provided. This template is copied and edited to include your site-specific information. Then it is run to install the automatic start-up facility.
The installation tools and documentation is located in $MMOD_ROOT/inst/ bminrd.
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APPENDIX 4 MacroModel Atom and Bond Types
4.1 BONDS
The following is a list of the values that may appear in the MacroModel structure file format for bond orders and the corresponding meaning of these values.
Value Symbol Description 0 . Zero order bond 1 - Single Bond 2 = Double Bond 3 % Triple Bond 4 * Bond of Undefined Order (excluding zero order)
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4.2 ATOMS
No Symbol Description Equivalencies MM2/ Charmm Amber MM3 1 C1 Carbon - SP 4 2 C2 C - SP2 2,3 CT,C C,C*,CA,CB, CC,CM,CF,CG ,CN 3 C3 C - SP3 1 CT CT 4 CA United atom CH CH1E CH - SP3 5 CB United atom CH2 CH2E C2 - SP3 6 CC United atom CH3 CH3E C3 - SP3 7 CD United atom CH CR1E CD,CE,CJ,CP - SP2 8 CE United atom CH2 - SP2 9 CF United atom CH - SP 10 CM Carbanion 11 CP Carbocation 30 12 CR Carbon free 29 radical 13 14 C0 Any Carbon 15 O2 Oxygen - Dou- 7 O O,O2 ble Bond 16 O3 O - Single 6 OH1,OH2 OS,OH Bonds 17 OA United atom OH OH1E 18 OM O- (alkoxide, 47 OC carboxylate)
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19 OW United atom H2O OH2E - Water 20 OP Oxonium (sp2) =O+- 21 OQ Oxonium (sp3) R3O+ 22 23 O0 Any Oxygen 24 N1 Nitrogen - SP 10 25 N2 N - SP2 9 N,NR,NP,NH N,NB,NC,N*, 1,NH2 N2 26 N3 N - SP3 8 NH3 NT 27 NA United atom NH - SP3 28 NB United atom NH2 NH1E - SP3 29 NC United atom NH3 - SP3 30 ND United atom NH2 NH2E - SP2 31 N4 N+ - SP2 NC2 NA 32 N5 N+ - SP3 39 N3 33 NE United atom NH+ - SP3 34 NF United atom NH2+ - SP3 35 NG United atom NH3E NH3+ - SP3 36 NH United atom NH+ - SP2
37 NI United atom NC2E NH2+ - SP2 38 39 40 N0 Any Nitrogen
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41 H1 H-Electro- 5,44 HA HC,HS neut(e.g. C,S) 42 H2 H-O(Neut) 21,24 H,HC HO 43 H3 H-N(Neut) 23,28 H,HC H,H2 44 H4 H-Cation 48 MM3 H3 (none in MM2)
45 H5 H-Anion 46 47 48 H0 Any Hydrogen 49 S1 Sulfur 15,17, S S,SH 18
50 SA United atom SH SH1E 51 SM Thiolate anion 52 S0 Any Sulfur S 53 P0 Phosphorus 25 P 54 B2 Boron (sp2) 26 55 B3 Boron (sp3) 27 56 F0 Fluorine 11 57 Cl Chlorine 12 58 Br Bromine 13 59 I0 Iodine 14 60 Si Silicon 19 61 Du Dummy atom for FEP 62 Z0 Special Atom to be defined 63 Lp Lone Electron LP Pair 64 00 Any Atom 0 *
Note: 00 atoms stored as type 0 in atom connection table.
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Note: All current force fields require explicit hydrogens on heteroatoms.
See the BatchMin Reference Manual for a description of the atom.typ file and how to add additional atom types to MacroModel.
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APPENDIX 5 MacroModel Structure File Format
A MacroModel molecular structure file contains one or more entries each describ- ing a molecule or set of molecules. Each entry of an uncompressed file begins with a header line giving the number of atoms in the entry and an optional name for the structure. Following the header line are series of atom entries. Each atom entry line describes one atom and the number of such entries is equal to the num- ber of atoms in the structure. Atoms are numbered sequentially.
Structure files may also contain compressed entries. In a compressed file the first entry is a standard uncompressed entry. Succeeding entries are in the compressed format. See below for details on the uncompressed format.
A file may contain one or more entries. Each time the structure is read, one full entry is loaded into MacroModel or BatchMin. As of Version 5.0 we are supply- ing a library (called MMIO) which supports the reading and writing of files in the MacroModel format. We use this library for all of our programs. See the Macro- Model Technical Manual for more details. This library also allows for the reading of compressed files which were added as of Version 5.0. All reading and writing of MacroModel structure files should be done using the MMIO library. By using the library users will be guaranteed of compatibility with any changes to the format of the files. Users will simply need to relink their code with a new version of the library. The MMIO library is located in $MMOD_ROOT/develop/lib. Include files for MMIO are located in $MMOD_ROOT/develop/include.
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5.1 MacroModel Uncompressed File Format
The following description pertains to the uncompressed format. Also, the formats described below are FORTRAN format statements.
Entry Header Line (first line of file or entry) FORMAT(1X,I5,2X,A70)
I5 NIATMS (INTEGER*4) - The number of atoms in the entry A70 (CHARACTER*70) - The text name of the entry (optional)
Atom Entries
Atom entries start from line 2 and continue until line NIATMS + 1. Each line rep- resents one atom.
FORMAT(1X,I3,6(1X,I5,1X,I1),1X,3(F11.6,1X),I5,2A1,I4,2F9.5,1X,A4,1X,A4) I3 (INTEGER*4)The MacroModel atom type number (e.g. 3 = sp3 carbon) 6(1X,I5,1X,I1)Describing up to 6 attached atoms as follows:
I5 (INTEGER*4) The atom sequence number of an at- tached (bonded) atom I1 (INTEGER*4) The order of the bond to the attached atom (0 = zero order [used for transition states and coordination complexes], 1 = sin- gle bond, 2 = double bond, 3 = triple bond).
3(F11.6,1X) Cartesian coordinates for this atom:
F11.6 (REAL*4) - X-coordinate in Angstroms. F11.6 (REAL*4) - Y-coordinate in Angstroms. F11.6 (REAL*4) - Z-coordinate in Angstroms.
I5 (INTEGER*4) - Optional residue number (used only with biopolymers). A1 (CHARACTER*1) - Optional single-character MacroModel residue code (see below). A1 (CHARACTER*1) - Optional single-character residue chain name. I4 (INTEGER*4) - Optional atom color (see below). If no color is given, then MacroModel will give the atom a standard atom type-based color. 2F9.5(REAL*4) - Optional atomic charge in electron units (BatchMin will re- compute charges unless CHGF option used). First charge is used for stan- dard charge/charge electrostatics, second charge is used in conjunction with charge/multipole electrostatics. A4 (CHARACTER*4) - Optional ascii residue name (e.g. PDB residue name)
154 MacroModel User Manual Version 7.0 MacroModel Atom Color Table
A4 (CHARACTER*4) - Optional ascii atom name (e.g. PDB atom name)
MacroModel Atom Color Table
The following are pertinent when running MacroModel in 3D GL mode.
Number Color Name Red Green Blue 0 Color undefined 0 0 0 1 Black 0 0 0 2 Grey 140 140 140 3 Dark blue 0 0 255 4 Blue 20 20 255 5 Light Blue 100 100 255 6 Aqua 112 219 147 7 Turquoise 173 234 234 8 Blue-green 0 255 127 9 Dark green 0 100 0 10 Green 0 255 0 11 Light green 50 204 50 12 Yellow-green 153 204 0 13 Yellow 255 255 10 14 Orange 234 130 50 15 Dark red 142 35 107 16 Red 255 0 0 17 Pink 255 100 100 18 Red-purple 234 173 234 19 Purple 255 0 255 20 Blue-purple 159 95 159 21 White 255 255 255 Table 13. MacroModel RGB Values for 3D GL Mode
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MacroModel/PDB Residue Types
Residue Name BrookHaven MacroModel 3-Character Code 1-Character Code ALANINE ALA A ASP OR ASN ASX B CYSTEINE CYS C ASPARTIC ACID ASP D GLUTAMIC ACID GLU E PHENYLALANINE PHE F GLYCINE GLY G HISTIDINE HIS H ISOLEUCINE ILE I HOMOSERINE HSE J LYSINE LYS K LEUCINE LEU L METHIONINE MET M ASPARAGINE ASN N HYDROXYPROLINE HYP O PROLINE PRO P GLUTAMINE GLN Q ARGININE ARG R SERINE SER S THREONINE THR T HYDROXYLYSINE HYL U VALINE VAL V Tryptophan TRP W Unusual or unknown UNK X residue Tyrosine TYR Y GLU or GLN GLX Z Ornithine ORN 1 Sarcosine SAR 2 Taurine TAU 3 Table 14. MacroModel/PDB Residue Types
156 MacroModel User Manual Version 7.0 MacroModel/PDB Residue Types
Thyroxine THY 4 Beta alanine ALB 5 Phosphate PHO 6 Pyroglutamic acid PCA 7 Acetyl ACE 8 Formyl FOR 9 Water HOH 0 Adenosine A a Cytidine C b Guanosine G c Uridine U d 1-Methyladenosine 1MA e 5-Methylcytidine 5MC f 2'-O-Methylcytidine OMC g N(2)-Methylguanosine 2MG h N(2)-Dimethylgua- M2G i nosine 7-Methylguanosine 7MG j 2'-O-Methylguanosine OMG k Ribosylthymidine 5MU l Dihydrouridine H2U m Pseudouridine PSU n Wybotosine YG o Thymine T p Table 14. MacroModel/PDB Residue Types
5.2 MacroModel Compressed Entry Format
The following is a description of the MacroModel compressed format. Note that you must have one uncompressed entry at the beginning of your structure file. When using MMIO the library will automatically do this for you. All reading and writing of structure files should be done via MMIO. See section 5.1 on page 154.
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Entry Header Line (first line of file or entry) FORMAT(1X,I5,2X,A70)
I5 NIATMS (INTEGER*4) - The number of atoms in the entry. This number is preceded by a ’-’ (minus sign) and is typically smaller than the total number of atoms in the uncompressed version. A70 (CHARACTER*70) - The text name of the entry (optional)
Atom Entries
Atom entries start from line 2. Only atoms with information that has changed need to be entered. The only fields that are allowed to vary are the X,Y, Z coordi- nates and color.
FORMAT(I5, 1X, 3(F11.6,1X), I4) I5 (INTEGER*4) The number of the affected atom. 3(F11.6,1X) Cartesian coordinates for this atom:
F11.6 (REAL*4) - X-coordinate in Angstroms. F11.6 (REAL*4) - Y-coordinate in Angstroms. F11.6 (REAL*4) - Z-coordinate in Angstroms.
I4 (INTEGER*4) - Optional atom color (see below). If no color is given, then MacroModel will give the atom a standard atom type-based color.
Please be aware that the compressed file format is subject to change. It is to your advantage to use MMIO which will insulate you from any changes to the for- mat. This will also minimize future work on your part as a simple relinking of your code with MMIO will be all that is necessary.
158 MacroModel User Manual Version 7.0 User Manual Index
A Cntr 91 ABool 101 ComFl 64 AddIA 74 Compressed MacroModel Files 29 AddLb 46, 87 conformational 53 ADist 43, 86 Conformationally Flexible Molecules 53 ALab 45 Constrained Torsion Angle(s) 74 AMBER* 58 Contour Panel 91 AMBER94 59 Control Window 15, 36 Atm 73 Convergence 62 Atom Numbers 86 convergence 62 atom.typ 56 CPK 45 autorotation 35 CPK Resize 48 AveAt 87 Crystal Eyes Stereo 14 CSRCH 78 B CtrlWin 37 ball-and-stick 45 BAngl 43, 86 D BATCH_ROOT 145 DAngl 43, 86 BatchMin 13, 57, 125 DefAx 41 BatchMin Network Server Installation Instructions 134 DELET button 22 Boolean 101 Depth 37 Boolean Operations on Atom Sets 101 Depth Cue 37 bump checking 44 DFile 90 BumpCheck 45 Differences in force field equations 58 BumpCheckClose 45 Differences in parameters 59 Docking 40, 90 C Dot Surfaces 90 C Tor 75 DRIV 91 Cambridge Crystal File 29 DYNAMC 76 CCrit 72 dynamics 75 Chem3D 98 Chirl 79 E Clear 86 ECalc 71 Clip 31, 34 EdgeD 74 clipping 37 Energetic Tasks 70 Close 78 Energy Calculation 71 Cmpre 79 ENRGY 63 CNNCT 52 Examining BatchMin COM Files 64 CNSTR 75 eXodus 121
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Extended Atom Types 56 M Macintosh 121 F MacroModel Force Fields 57 FAtm 86 MacroModel Windows 15 FFVIEW 79 MacX 121 File Reading 25 Main Button Panel 18 file selector 26 Main Structure Window 17 File Writing 27 Manual Molecular Construction 52 Filtr 88 MBool 102 FinlT 76 MCrlo 78 FMNR 72 MCSD 76 force field 58, 145 MCSM 78 Foreign Structure Files 28 MDyn 76 FRes 86 message window 16 FUSE 52 MINIM 71, 74, 75, 79 FxCol 74 MM2* 58 MM3* 58 G MMFF 59 GB/SA 61 Mode Options Window 18 GEOM 86 mode options window 18 global rotation 34 Modifying Existing Structures 50 Global Transformations 33 Molecular Complex Construction and Docking 53 Global XY Rotations 30 molecular mechanics 57 Gradient Calculation 71 Molecular Translations and Rotations (Docking) 40 Mols 76, 78 H Monitoring BatchMin Energetic Tasks 68 Montr 68, 69 Halting BatchMin Tasks 69 Movie 105 hardware stereo 47 Multiple BatchMin Operations 64 Hbond 105 Help and Documentation 20 Host 65, 67 N hostfiles.dat 65 NAtm 86 How the NFS Style Remote BatchMin Facility Works 128 NRes 86 HPref 105 NUM 86 Num 86 I NxtOp 64 InitT 76 Input Mode and General Operation 15 O IRIS RGB 98 Open 27 It/S 72 Operation of the 3-Button Mouse 32 OPLS* 58 L Opt 17, 20, 24, 31, 32, 34, 35, 37, 44, 45, 46, 47, 48, 49, 54 LayoutSave 24 Orient 41
160 MacroModel User Manual Version 7.0 OSF/Motif Window Manager 23 SGI RGB 98 SHAKE 77 P Shel1 73 PC 121 SimuT 77 PDB 28 Sleep 69 Photo 106 Solvation Treatment 61 Pixelmap plotting 99 solvent files 145 Plot 98 Start 66, 71, 72 Plot1D 94 Starting BatchMin Energetic Jobs 65 plots 99 Stereo 47 polytube 45 Stop 69 Polytube Diagrams 46 Structural Rendering Options 45 Popup Prompt 20 Structure Building 49 PostScript 98 structure building 49 PRCG 71 structure file 153 Putting BatchMin Tasks to Sleep 69 Structure File Reading and Writing 24 Structure Files from External Sources 51 R Structure Input 22 Ramachandran 91 Structure Plotting 98 rbm 143 SUBED 73 rbmin 143 Submode Options Window 19 READ 24 Subs 73 Real Time Molecular Translations and Rotations - TRMol SubsM 74 Button 42 Substructure Energy Minimization 73 RemIA 74 SURFAC 91 Remote Procedure Call 134 SURFAC submode 90 Renam 54 SYBYL MOL2 28 Reset 34, 75 Symtry 78 RGB 48, 98 SYSTEM 23 Ribbn 103 ribbon diagrams 103 T Ribbon Panel 103 TBond 78 Rocking 35 Terminating BatchMin Energetic Tasks 69 Rot T 38 Textual Captions 87 RPC 143, 146 ThickBond 45 TiStp 77 S TiTot 77 Sampl 77 TNCG 72 SBCFl 74 Torsion Angle Rotations 37 Scale 31, 34 TRAll 43 Scaling and XY Clipping 31, 32 TRMol 42 SelRs 73 Set Colors 48 V Setting Up BatchMin Energetic Jobs 63 ViewSave 35
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Volume Boolean Operations On Molecules 102 WRITE 24, 27 volumes 102 X W X Emulators 31 wire frame 45 X-terminals 9 Wireframe 99 XVision 124
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3D Control Window and Mouse/Keyboard Controls
3D Control Window g Control Control Rot T TR Mol TR All a a Top View SSFront View b
c f d
e
a - Toggle button to switch between Top View and Front Vieww b - Back clipping plane c - Z-clipping slab thickness (controls separation of clipping planes)
d - Z-translation of molecule through Z-clipping slab e - Front Z-clipping plane
f - XY scaling (centered on origin atom)) g - Transformation toggle buttons. Rot T is used to Rotate a Torsion TR Mol is used to Translate/Rotate Molecules TR All is used to Translate/Rotate ALL (molecules with TR icons)
MacroModel 3D - Mouse/Keyboard Functions
Torsional Rotations (Rot T) Left Button - Pick two atoms on bond or bond to be rotated. Yellow torsional icon produced. Middle Button depressed: Select torsional icon and control torsional rotation.
LMR Molecular Translations and Rotations (TRMol) Left Button - Pick atom in molecule to be moved. Purple molecular icon produced. Mouse Middle Button depressed: Select molecular icon and control XY molecular translation. Left Button picks menu buttons "T" also depressed: Z molecular translation and atoms; also selects default