Jaguar Quick Start Guide
Contents
1. 8 2 6 Cleaning Up the Geometry msronrarnvrvrvenvrnnnrnnvnnnrvenrennrrernrnnerersernnneneenesrensenesvensen 9 2 7 Building a Structure by Growing Fragments nennen 10 2 8 Building a Structure by Drawing 242404nsennnnnnnnennennnnnennnnnnnnnnnnn 11 2 9 Adjusting Bond Orders and Adding Hydrogens nn 12 2 10 Symmetrizing a Structure snsnsesensensnnennennenennennnnnnnnnnnnnnnnnannnnnn 13 Chapter 3 Running Jaguar Calculations 2 senere 15 3 1 Single Point Calculation 2s2442r4mennannanannannnnnnnannnnannannnnannnnnnannannnn 15 3 2 Geometry Optimization With DFT 444440nnnnnenennennnnnennnnnnnnnnnnnnn 16 3 3 Localized MP2 Energy Calculation 444440nnnnnnnnnnennnnnnnnnnnnnn 18 3 4 Displaying Orbitals in Maestro cece aaea es merne 19 3 5 Transition State Search oon eee ana ananas nene eee ee reve e rere eee e eren eee eren enen 23 3 6 Vibrational Frequencies gt s s smssammspsnssssnpessss sitsen ers oss NEN Snr NER 25 Jaguar 7 6 Quick Start Guide Contents 3 7 Intrinsic Reaction Coordinate Ca CU la ti ON uaaaaaan na ana aaa nena aneeeneee nennen 3 8 Prediction of pk Values a iiciciivisosoist esi ssiori n dos Ghh s n r ves b v n tie sd nda shend Getting Help ps rac n er n n n r v n Jaguar 7 6 Quick Start Gui2. 12 3 Click once in the Workspace An asterisk appears enclosed in a purple cube This cube marks the active drawing atom When there is an active drawing atom clicking again in the Workspace while in Draw mode places another atom and bonds it to the original atom Clicking a second time on the active drawing atom makes it inactive 4 Draw a six membered ring by clicking in the Workspace five more times in the proper configuration then clicking on the first atom As you move the mouse a yellow line connects the pointer to the active atom The atoms are all placed in the same plane 5 Click the first atom a second time to end the draw operation 2 9 Adjusting Bond Orders and Adding Hydrogens In this exercise you will adjust the C C bond orders and add hydrogen atoms to the skeleton structure that you drew You could also create the double bonds and add the hydrogens using Draw mode 1 Click the Increment bond order button on the Build toolbar Go The B below the cursor box indicates that the current selection state is Bonds 2 Click a bond in the structure you just drew The line representing the bond on which you clicked should now appear as a double line 3 Click two more bonds to create a structure with alternating double bonds 4 Double click the Add hydrogens button H The double click applies the selected hydrogen treatment to all atoms The default treat ment is All atom with No Lp You can
3. 4805803881000 0 0663006742000 kd 4 lal OK Cancel Preview Help Figure 3 3 The Edit Job panel showing the new gen section contents 3 4 Displaying Orbitals in Maestro Maestro can display surfaces including orbital and density plots generated by Jaguar In this exercise you will see how to produce and display orbital plots You will use the output from the DFT calculation you ran earlier to generate and display a surface plot of the HOMO and LUMO of benzene The generation of surfaces require a wave function For this exercise the wave function is obtained from the restart file but surfaces can be generated at the end of any job However no SCF iterations are needed so an initial guess calculation is sufficient to generate the surfaces 1 Read the restart file benzene dft 01 in as Geometry and settings A new project entry is created and included in the Workspace 2 From the menu choose Jaguar gt Initial Guess Only 3 In the Theory tab check that the level of theory is DFT Jaguar 7 6 Quick Start Guide 19 Chapter 3 Running Jaguar Calculations Lloji Use structures from Workspace included entries NM Files Browse Molecule Theory SCF Properties Output Properties select to edit options ee ps Surfaces MO density potential Atomic electrostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpol
4. Maestro 1 2 3 Ensure that the transition state entry is the only selected entry in the Project Table Choose Applications gt Jaguar gt Single Point Energy in the main window Choose Selected entries from the Use structures from option menu Jaguar 7 6 Quick Start Guide 25 Chapter 3 Running Jaguar Calculations 26 10 In the Properties tab select the check box for Vibrational frequencies Click Start The Start dialog box opens optional In the Job section choose a host from the Host option menu Set the name to trans freq and click Start This job takes several minutes to finish and generates a vib file that Maestro uses for animation of frequencies When the results are incorporated a V is added to the Aux col umn in the Project Table for the incorporated entry Click the V button in the Aux column of the project table for the incorporated entry The Vibration panel is displayed Select the first frequency in the list then select Animate This is the imaginary frequency that corresponds to the transition state The frequency is animated in the Workspace as if it were real The structure can be rotated in the Work space to view the animation from an optimal angle Click on other frequencies in the list to animate them Experiment with adjusting the speed and amplitude You do not need to deselect Animate to change to a different frequency The file trans_freq out contains a li
5. Wh one H ty orn 055509 an use yt I H e g 2 te wu 0 An J Grow Direction forward Joining Geometry anti IN Close Help Figure 2 3 The Build panel showing the Fragments tab Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro Figure 2 4 The methylamine molecule showing the grow bond 3 Select Grow 4 In the Organic library click the Amine fragment An amine group is placed in the Workspace The green arrow marks the grow bond 5 Click the Methyl fragment A methyl group is attached to the amine group 6 Create a Project Table entry named methylamine See Section 2 3 on page 7 if you unsure of how to do this 2 8 Building a Structure by Drawing In this exercise you will draw a benzene molecule in the Workspace Although drawing benzene is not necessary because there is a benzene fragment in the organic fragment library drawing structures can be useful when it is difficult to build them from fragments such as structures with multiple fused rings 1 Clear the Workspace 2 Click the Draw structures button on the Build toolbar f al The button is indented to indicate that Draw mode is active The default atom selected for drawing is carbon If you want to choose a different atom click and hold on the button and select an element from the menu that is displayed Jaguar 7 6 Quick Start Guide 11 Chapter 2 Building Small Molecules In Maestro
6. build structures in the Workspace during the exercises that follow you can save the structures in this project for later use Jaguar 7 6 Quick Start Guide 3 4 Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro This chapter contains exercises on building new molecular structures from fragments and from individual atoms You will use the structures you build in these exercises in the next chapter to run various Jaguar calculations For more detailed information about the Maestro Build panel tools see Chapter 4 of the Maestro User Manual Before starting you should ensure that the Default representation in the Settings tab of the Molecular Representation panel is Wire You can open this panel from the Display menu 2 1 Building a Structure by Placing Fragments This exercise demonstrates how to build a structure from fragments using Place mode In this mode you can place molecular fragments in the Workspace and substitute fragments in a structure in the Workspace 1 If the Build toolbar is not displayed at the top of the Workspace click the Show Hide the build toolbar button 7 The Build toolbar is now displayed at the top of the Workspace 2 Select the carbonyl fragment D HH The fragments are shown as full molecules with H atoms added to the fragment to com plete the molecule The H atoms are replaced when you join fragments The carbonyl fragment therefore appears as a formaldehyde molecu
7. structures If you have not yet built these structures build them now 1 In the Project Table panel shift click to select the alcohol and aldehyde entries and click the In box of the alcohol entry Choose Applications gt Jaguar gt Transition State Search in the main window Click Reset In the Molecule tab check that the basis set is 6 31G Choose Off from the Symmetry option menu au EN In the Theory tab make selections for a BLYP DFT calculation BLYP is in the Gradient corrected option menu Jaguar 7 6 Quick Start Guide 23 Chapter 3 Running Jaguar Calculations Jaguar CES Use structures from Workspace included entries M Files Browse Molecule Theory SCF Optimization Transition State Properties Solvation Output Search method Standard LST QST Structures Transition state nn I Reactant FREE Choose Product o Initial LST guess o 5 Search along Reactant product path ly Eigenvector LI Follow same eigenvector Low frequency modes le Job B3LYP 6 31G Transition State Search start Read Write Edit Reset Close Help Figure 3 8 The Transition State tab 7 In the Transition state tab see Figure 3 8 under Search method select LST The Reactant and Product rows in the Structures section are now available 8 In the Reactant r
8. Jaguar 7 6 Quick Start Guide O Schr dinger Press Jaguar Quick Start Guide Copyright 2009 Schr dinger LLC All rights reserved While care has been taken in the preparation of this publication Schr dinger assumes no responsibility for errors or omissions or for damages resulting from the use of the information contained herein Canvas CombiGlide ConfGen Epik Glide Impact Jaguar Liaison LigPrep Maestro Phase Prime PrimeX QikProp QikFit QikSim QSite SiteMap Strike and WaterMap are trademarks of Schr dinger LLC Schr dinger and MacroModel are registered trademarks of Schr dinger LLC MCPRO is a trademark of William L Jorgensen Desmond is a trademark of D E Shaw Research Desmond is used with the permission of D E Shaw Research All rights reserved This publication may contain the trademarks of other companies Schr dinger software includes software and libraries provided by third parties For details of the copyrights and terms and conditions associated with such included third party software see the Legal Notices for Third Party Software in your product installation at SSCHRODINGER docs html third party legal htmi Linux OS or SCHRODINGER docs html third_party_legal htm Windows OS This publication may refer to other third party software not included in or with Schr dinger software such other third party software and provide links to third party Web sites linked sites Refer
9. arizability v Oo urfaces Electrostatic potential Box size adjustment 0 0 A side Average local ionization energy Grid density pts A Energy units un kcal mol X Electron density Spin density 3 Molecular orbitals 2 00 g 2 00 2 00 2 00 u 0 00 0 00 0 00 l 0 00 4 0 00 gt Job blyp 6 31g Initial Guess Only Write Edit Reset Close Help Start Read Figure 3 4 The Properties tab 4 In the Properties tab select the check box in the Surfaces row Controls for the selection of surfaces are displayed in the lower part of the tab If you have a wave function these controls include a list of orbitals with their occupation num ber and eigenvalue If you do not have a wave function the controls allow you to specify the range of orbitals to plot relative to the HOMO and the LUMO 5 Select Molecular Orbitals 6 From the Alpha list select orbitals 20 through 23 click 20 shift click 23 Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations 10 11 12 13 Click Start The Start dialog box opens optional In the Job section choose a host from the Host option menu Type benzene_mo in the Name text box choose Replace existing entries from the Incor porate option menu then clic
10. cohol and the last six are from the backward direction moving toward the aldehyde structure To view the reaction in the ePlayer the entries must first be sorted It is also useful to display the structures in Ball amp Stick representation 1 In the Project Table include all 13 output structures in the Workspace To do this click the In column for the first entry and shift click the last entry 2 Double click the Draw atoms in ball and stick button on the main toolbar s 3 Clear the Workspace 4 In the Project Table click the Sort button on the toolbar A ZN The Sort Project Table panel is displayed 5 Select Rxn coord as the Primary Key and change the Order to Descending Sort Project Table Primary key Secondary key 1 none Enthalpy 298K Enthalpy kcal mol 298K molecular charge pKa atom QM Basis QM Energy QM Method Rxn Coord Spin multiplicity spin multiplicit Entropy 298K Entropy cal mol K 298K Entry ID Entry Name Free Energy 298K Free Energy kcal mol 298K Gas Phase Energy HOMO Order ascending Jr Sort Selected Rows Sort All Rows C Select only top e rows Order Ascending x Close Help Figure 3 11 The Sort Project Table panel Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations 6 Click Sort Selected Rows then clic
11. de Document Conventions In addition to the use of italics for names of documents the font conventions that are used in this document are summarized in the table below Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons and labels Monospace SSCHRODINGER maestro File names directory names commands envi ronment variables and screen output Italic filename Text that the user must replace with a value Sans serif CTRL H Keyboard keys uppercase Links to other locations in the current document or to other PDF documents are colored like this Document Conventions In descriptions of command syntax the following UNIX conventions are used braces enclose a choice of required items square brackets 1 enclose optional items and the bar symbol separates items in a list from which one item must be chosen Lines of command syntax that wrap should be interpreted as a single command File name path and environment variable syntax is generally given with the UNIX conven tions To obtain the Windows conventions replace the forward slash with the backslash in path or directory names and replace the at the beginning of an environment variable with a at each end For example SCHRODINGER maestro becomes 3SCHRODINGER maestro In this document to type text means to type the required text in the specified location and to enter text means to type the requir
12. e transition state structure Choose Applications gt Jaguar gt Reaction Coordinate in the main window You must choose the task after reading the input file because reading an input file with its settings sets the Jaguar task to the task defined by the gen section of the input file In the Properties tab clear the Vibrational frequencies check box In the IRC tab click Choose in the Transition state row of the Structures section The Choose Entry dialog box is displayed Select the structure you just read in Click Choose in the Reactant row of the Structures section and select the original alco hol entry If the alcohol structure is not listed in the Choose Entry panel then select All from the Choose entry from menu Click Choose in the Product row and select the original aldehyde entry Click Start The Start dialog box opens optional In the Job section choose a host from the Host option menu Jaguar 7 6 Quick Start Guide 27 Chapter 3 Running Jaguar Calculations 28 13 Set the name to irc choose Append new entries as a new group from the Incorporate option menu and click Start The job takes a few minutes When the job finishes 13 new entries are incorporated into the Project Table as an entry group named irc and are selected The first entry corresponds to the transition state structure the next six are the geometries found moving in the forward direction from the transition state to the al
13. ectory and create a project These tasks are described in the following sections 1 1 Creating a Working Directory The first task to be done in preparation for the tutorial is to create a working directory to keep all your input and output files UNIX 1 Change to a directory in which you have write permission cd mydir Create a directory by entering the command mkdir directory name Jaguar 7 6 Quick Start Guide 1 Chapter 1 Getting Started Windows 1 Open the folder in which you want to create the folder that serves as your working direc tory The default working directory used by Maestro is your user profile which is usually set to C Documents and Settings username on Windows XP and 2000 and to C Users username on Vista To open this folder do the following a Choose Run from the Start menu b Enter 3USERPROFILE in the Open text box and click OK 2 Click Make a new folder under File and Folder Tasks You can also choose Folder from the New submenu of the File menu 3 Enter a name for the folder If you want to create a folder inside this folder repeat this procedure 1 2 Starting Maestro Once you have created the working directory you can start Maestro UNIX 1 Set the SCHRODINGER environment variable to the installation directory csh tesh setenv SCHRODINGER installation path bash ksh export SCHRODINGER installation path This environment variable is also required to r
14. ed text then press the ENTER key References to literature sources are given in square brackets like this 10 Jaguar 7 6 Quick Start Guide v vi Jaguar 7 6 Quick Start Guide Chapter 1 Getting Started This manual contains exercises designed to help you learn the basic tasks you will need to prepare and initiate Jaguar calculations from Maestro For more information about Jaguar features see the Jaguar User Manual This chapter contains instructions for setting up the tutorial Chapter 2 contains exercises on building new molecular structures which are used in the calculations in the next chapter Chapter 3 provides a set of exercises that show you how to run various Jaguar calculations single point energies with both DFT and LMP2 theory geometry optimizations transition state searches intrinsic reaction coordinate calculations frequency calculations orbital plot ting and pK prediction Help for each of the Jaguar tasks is available in the Maestro online help To do the exercises you must have access to an installed version of Maestro 9 0 and Jaguar 7 6 For installation instructions see the Installation Guide The directory in which the software is installed will be referred to as the installation directory The preparations that must be made for the exercises are to create a working directory to keep all your input and output files start Maestro ensure that this directory is Maestro s current working dir
15. ences to such other third party software or linked sites do not constitute an endorsement by Schr dinger LLC Use of such other third party software and linked sites may be subject to third party license agreements and fees Schr dinger LLC and its affiliates have no responsibility or liability directly or indirectly for such other third party software and linked sites or for damage resulting from the use thereof Any warranties that we make regarding Schr dinger products and services do not apply to such other third party software or linked sites or to the interaction between or interoperability of Schr dinger products and services and such other third party software Revision A October 2009 Contents Document CONVENtiONS win uar anen Gjendet de dt NE v Chapter 1 Getting Sartre learn ERE 1 1 1 Creating a Working Directory ccc seeren 1 1 2 Staring Maestro aa seen 2 1 3 Setting the Maestro Working Directory css suser 3 1 4 Creating a Maestro PrOjeCt s sse sisssisss nsssssssrssstesvisssdrissensbrsssssbiseninsssrtsiesensnrsnsriner 3 Chapter 2 Building Small Molecules In Maestro 5 2 1 Building a Structure by Placing Fragment scenens 5 2 2 Adjusting a Dihedral Angle mnmrernennennnnnnnennnnnnnnnnnennnnennnnnnnn nennen 6 2 3 Saving Workspace Contents as a Project Entry ne 7 2 4 Duplicating Project Entries gjaqe n 7 2 5 Converting the Acetaldehyde Structure Into Vinyl Alcoho
16. et the isovalue to 0 05 Click Display Options The Display Options dialog box is displayed This dialog box has controls for the style transparency and color scheme Experiment with changing the transparency the style and the colors of the positive and negative lobes For this manual the colors of the surfaces were changed for better grayscale printing Display the remaining two orbitals To save images of the Workspace like those shown in Figure 3 6 choose Maestro gt Save Image then make settings and supply a filename in the Save Image panel Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations 7 Surface Display Options Transparency Front surface J 0 BEE Adjust together Negative color Blue Back surface Q fo Style Solid Mesh Dot Color scheme Property Partial Charge M Constant Color Red T Set as default 7 set as default Map values from volume data benzene orbs MO 23 Color ramp Red Wi ite Blue z Minimum Reset Full Range Figure 3 7 The Display Options dialog box 3 5 Transition State Search In this exercise you will model the interconversion between acetaldehyde and vinyl alcohol which involves the transfer of a proton from the methyl group to the carbonyl oxygen You will use the vinyl alcohol and acetaldehyde molecules that you built in Chapter 2 as the starting and ending
17. f the ring to be excited into an expanded virtual space a semi delocalized LMP2 This can be achieved automatically by adding keywords directly to the input file 4 Click Edit The Edit Job panel is displayed 5 In the amp gen section add idelocv 1 and ireson 1 6 Click OK 7 In the Jaguar panel click Start The Start dialog box opens 8 optional In the Job section choose a host from the Host option menu 9 Type benzene_mp2 in the Name text box and click Start This LMP2 job takes several minutes When the job has finished close the Monitor panel 10 Examine the output file benzene_mp2 out using a text editor Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations File Edit Help Edit Input file Structure BEE amp gen basis 6 31g mp2 3 Fa idelocv 1 ireson 1 amp amp zmat cl 1 2002314708000 0 7951057678000 0 0414783553000 c2 1 3206721010000 0 6052771144000 0 0055367871000 c3 0 1678722364000 1 4091648794000 0 0335616141000 c4 1 1053831025000 0 8127361885000 0 0367544691000 cs 1 2257902210000 0 5875734174000 0 0008028323000 c6 0 0730021844000 1 3914970293000 0 0383210210000 H7 2 0967963987000 1 4204434914000 0 0718974100000 H8 2 3108964998000 1 0692396240000 0 0079968055000 H9 0 2615870999000 2 4982390021000 0 0615315895000 H10 2 0019410769000 1 4380876308000 0 0672203624000 H11 2 2159506374000 1 0514731434000 0 0032692881000 a a 0 1666842277000 2
18. guar 7 6 Quick Start Guide 13 14 Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations This chapter is designed to introduce you to the main capabilities of Jaguar 7 6 and its interface with Maestro 9 0 3 1 Single Point Calculation The default single point energy calculation set up in Maestro is a density functional calcula tion with the B3LYP functional and a 6 31G basis set The molecule is assumed to be singlet and uncharged To run a default calculation you can build or include a molecule in the Work space and submit the job with no special options In this exercise you will use the molecule that you built in Section 2 8 on page 11 If you have not done this exercise do so now 1 In the Project Table panel click the In column for the benzene entry The benzene entry is included in the Workspace and all others are excluded 2 From the Applications menu choose Jaguar gt Single Point Energy The Jaguar panel is displayed set up for a single point energy calculation The default structure as shown in the Use structures from option menu is the one in the Workspace 3 Click the Start button The Jaguar Start dialog box opens This dialog box provides controls for the running of the job and the incorporation of the results into Maestro By default the job name is the entry name and the job is run on the local host the host on which you are running Mae stro 4 In the Output section choose Inc
19. information you need in the Maestro help system check the following sources Maestro User Manual for detailed information on using Maestro Maestro Command Reference Manual for information on Maestro commands Maestro Overview for an overview of the main features of Maestro Maestro Tutorial for a tutorial introduction to basic Maestro features Jaguar User Manual for detailed information on using Jaguar Jaguar Frequently Asked Questions pages at https www schrodinger com Jaguar FAQ html Jaguar 7 6 Quick Start Guide 31 Getting Help 32 Known Issues pages available on the Support Center The manuals are also available in PDF format from the Schr dinger Support Center Local copies of the FAQs and Known Issues pages can be viewed by opening the file Suite 2009 Index html which is in the docs directory of the software installation and following the links to the relevant index pages Information on available scripts can be found on the Script Center Information on available software updates can be obtained by choosing Check for Updates from the Maestro menu If you have questions that are not answered from any of the above sources contact Schr dinger using the information below E mail help schrodinger com USPS Schr dinger 101 SW Main Street Suite 1300 Portland OR 97204 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com Ge
20. k Close 7 Click the Play forward button on the toolbar to start cycling through the entries The hydrogen atom moves away from the oxygen and the double bond rotates 8 From the Loop button menu on the toolbar choose Oscillate 4 t 9 Click the Play forward button 10 The sequence of structures is played in the forward direction then the reverse direction and continues this pattern 11 Click the Stop button You can change the speed of the ePlayer and set other options in the ePlayer Options panel which you open from the ePlayer menu 3 8 Prediction of pK Values In this exercise you will calculate the pK of methylamine using the structure you built in an earlier exercise 1 Include the methylamine molecule in the Workspace 2 From the Applications menu choose Jaguar gt pKa The Jaguar panel opens with the Molecule tab displayed The controls in this tab are sim plified In the lower section you can specify the pK atom Use this atom is selected by default 3 In the pKa atom section select Pick 4 Click on the nitrogen atom in the Workspace The nitrogen atom is marked and its label is displayed in the text box 5 Select Workspace from the Use structures from option menu Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations Jaguar Lellallxl Use structures from Selected structure files I Files nfs zonel dyall glide 2008ul structures S0ligs mae gz B
21. k Start When the job has finished close the Monitor panel The job takes about one minute The results are automatically incorporated and the first surface the HOMO is displayed in the Workspace Since both the HOMO and the LUMO are degenerate orbitals the orbital displayed could be either of the degenerate pair If the Project Table panel is not open click the Open Close project table button on the toolbar EH In the Project Table click the S button in the Aux column for the benzene entry The Manage Surfaces panel is displayed The Surface Table shows all the surfaces gener ated by the Jaguar job Click the V column for orbital 21 Orbital 21 replaces orbital 20 in the Workspace 7 Manage Surfaces benzene orb MO 20 0 209055 MO 20 benzene orb MO 21 0 209050 MO 21 171718 ERE benzene orb MO 22 0 020561 MO 22 0 05 benzene orb MO 23 0 020551 MO 23 0 05 i ap Import Duplicate Delete Limit Export to Map Display Options Isovalue G gt 0 05 O Display at most JA ee N Figure 3 5 The Manage Surfaces panel Jaguar 7 6 Quick Start Guide 21 Chapter 3 Running Jaguar Calculations 22 14 15 16 17 18 Figure 3 6 The degenerate benzene HOMO molecular orbitals Move the Isovalue slider The volume occupied by the orbital changes with the isovalue Res
22. le If you pause the pointer over the fragment the fragment name is displayed in the tooltip Balloon Help 3 Click in the Workspace A formaldehyde molecule is placed in the Workspace 4 Select the methyl fragment H HEH H Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro Distance Angle Dihedral a Define atoms for dihedral adjustment I Pick onda v PS fx Show markers 1 H5 C4 C1 5 4 1 2 Delete Delete All Reset Move All attached atoms All attached terminal atoms gt Only single atom Figure 2 1 The Dihedral tab in the Adjust panel 5 Click on one of the hydrogen atoms of the formaldehyde molecule in the Workspace The hydrogen atom is replaced with a methyl fragment 2 2 Adjusting a Dihedral Angle In this exercise you will change the orientation of the oxygen atom relative to the hydrogen atoms so that there is a hydrogen atom cis to the oxygen atom 1 Choose Edit gt Adjust gt Dihedral The Adjust panel is displayed with the Dihedral tab on top 2 Choose Bonds from the Pick menu 3 Click on the C C bond towards the carbonyl end The H C C O dihedral with the H trans to the O should be selected the dihedral angle should be 180 to within a sign The selected atoms appear in the table in the center of the Dihedral tab A broken line and an arrow mark the selected dihedral in the Work
23. ling documenta tion see the Installation Guide For information on running jobs see the Job Control Guide Maestro has automatic context sensitive help Auto Help and Balloon Help or tooltips and an online help system To get help follow the steps below Check the Auto Help text box which is located at the foot of the main window If help is available for the task you are performing it is automatically displayed there Auto Help contains a single line of information For more detailed information use the online help e If you want information about a GUI element such as a button or option there may be Balloon Help for the item Pause the cursor over the element If the Balloon Help does not appear check that Show Balloon Help is selected in the Maestro menu of the main window If there is Balloon Help for the element it appears within a few seconds For information about a panel or the tab that is displayed in a panel click the Help button in the panel or press F1 The help topic is displayed in your browser For other information in the online help open the default help topic by choosing Online Help from the Help menu on the main menu bar or by pressing CTRL H This topic is dis played in your browser You can navigate to topics in the navigation bar The Help menu also provides access to the manuals including a full text search the FAQ pages the New Features pages and several other topics If you do not find the
24. nerally e mail correspondence is best because you can send machine output if necessary When sending e mail messages please include the following information All relevant user input and machine output Jaguar purchaser company research institution or individual Primary Jaguar user e Computer platform type e Operating system with version number Jaguar version number Maestro version number e mmshare version number On UNIX you can obtain the machine and system information listed above by entering the following command at a shell prompt SSCHRODINGER utilities postmortem This command generates a file named username host schrodinger tar gz which you should send to help schrodinger com If you have a job that failed enter the following command SCHRODINGER utilities postmortem jobid where jobid is the job ID of the failed job which you can find in the Monitor panel This command archives job information as well as the machine and system information and Jaguar 7 6 Quick Start Guide Getting Help includes input and output files but not structure files If you have sensitive data in the job launch directory you should move those files to another location first The archive is named jJobid archive tar gz and should be sent to help schrodinger com instead If Maestro fails an error report that contains the relevant information is written to the current working directory The report is named maestr
25. ngdom SCHRODINGER
26. ngle bond Click the Increment bond order button on the Build toolbar Ga In the Workspace click on the C C bond The bond should now be represented by a double line indicating that the bond order has changed to double Click the Draw structures button on the Build toolbar 2 Lu Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro 9 In the Workspace click on the oxygen atom then click twice on the unbonded hydrogen A bond is drawn between the two atoms 2 6 Cleaning Up the Geometry In this exercise you will clean up the geometry by performing a force field calculation that provides good estimates of the bond lengths and angles e Click the Clean up geometry Build toolbar button i A dialog box is displayed that shows cleanup progress You should always clean up structures before optimizing them If the molecule has symmetry always symmetrize the molecule before cleaning up the geometry to guarantee perfect point group symmetry and to speed up the Jaguar calculation In this exercise the structure already has C symmetry so it is not necessary to symmetrize it To symmetrize a molecule choose Edit gt Symmetrize Workspace in the main window The changes to this structure should be automatically saved in the project If your project pref erences Project tab Preferences panel are not set to synchronize Workspace changes auto matically you should see a red exclamation
27. o_error txt and should be sent to help schrodinger com A message giving the location of this file is written to the terminal window More information on the postmortem command can be found in Appendix A of the Job Control Guide On Windows machine and system information is stored on your desktop in the file schrodinger_machid txt If you have installed software versions for more than one release there will be multiple copies of this file named schrodinger_machid N txt where N is a number In this case you should check that you send the correct version of the file which will usually be the latest version If Maestro fails to start send email to help schrodinger com describing the circumstances and attach the file maestro_error txt If Maestro fails after startup attach this file and the file maestro EXE dmp These files can be found in the following directory LOCALAPPDATA Schrodinger appcrash On Windows XP and Windows 2000 LOCALAPPDATA is not set by default but should correspond to SUSERPROFILE Local Settings Application Data Jaguar 7 6 Quick Start Guide 33 34 Jaguar 7 6 Quick Start Guide 120 West 45th Street 17th Floor 101 SW Main Street Suite 1300 8910 University Center Lane Suite 270 New York NY 10036 Portland OR 97204 San Diego CA 92122 ZeppelinstraBe 13 Dynamostra e 13 Quatro House Frimley Road 81669 Miinchen Germany 68165 Mannheim Germany Camberley GU16 7ER United Ki
28. ometry and wave function for the single point calculation performed in the last exercise 3 Ensure that Read As is set to Geometry and settings 4 Click Open In the Project Table a new entry benzene 01 has appeared and has been included auto matically in the Workspace You can view the input file information by clicking the Edit button in the Jaguar panel Do not change any of the settings but notice that in the guess section there is now a con verged wave function Close the panel by clicking Cancel Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations allel Use structures from Workspace included entries NM Files Browse Molecule Theory SCF Properties Solvation Output Level of theory DFT Density Functional Theory DFT Spin unrestricted Excited state TDDFT Number of excited states E Maximum TDDFT iterations E Grid density medium Jr Functionals Hybrid Bay v O Gradient corrected O LDA SVWN p O Specified in input file Job B3LYP 6 31G Single Point Energy Start Read Write Edit Reset Close Help Figure 3 2 The Theory tab of the Jaguar panel 5 Choose Applications gt Jaguar gt Optimization in the main window The Jaguar panel is displayed set up for a geometry optimization 6 In the Theory tab
29. orporate gt Append new entries individually The incorporation mode is persistent so the next time you run a job the mode selected is the last mode that you used 5 optional In the Job section choose a host from the Host option menu 6 Click Start The Monitor panel is displayed allowing you to monitor the progress of the job This job should take only a few seconds Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations 16 7 Jaguar Start Output Incorporate Append new entries as anew group job Name benzene Compose Host barbara 4 7 CPUs 1 Username dyall Scratch directory scr had stat cancel Help Figure 3 1 The Jaguar Start dialog box 7 When the job finishes close the Monitor panel The results of the job are incorporated into Maestro and a new entry named benzene appears in the Project Table 3 2 Geometry Optimization With DFT In this exercise you will optimize the geometry of the output structure from the previous exer cise at the BLYP 6 31G level 1 In the Jaguar panel click Read at the bottom of the panel The Jaguar Read file chooser is displayed If you do not have the Jaguar panel open choose Applications gt Jaguar gt Single Point Energy in the main window 2 Navigate to and select the Jaguar restart file benzene 01 in The restart file contains the ge
30. ow click Choose The Choose Entry dialog box is displayed 9 Select alcohol from the list then click Choose The dialog box closes and the Reactant text box now contains alcohol The alcohol entry has been selected as the reactant Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations 10 11 12 13 14 15 Figure 3 9 The transition state structure In the Product row click Choose The Choose Entry dialog box is displayed again Select aldehyde from the list then click Choose The dialog box closes and the Product text box now contains aldehyde The aldehyde entry has been selected as the product In both rows click the box to the left of the text box The aldehyde structure is displayed in the Workspace on top of the alcohol structure Click Start The Start dialog box opens optional In the Job section choose a host from the Host option menu Set the name to trans_state choose Append new entries individually from the Incorpo rate option menu and click Start Convergence should be reached in about 13 15 geometry steps When the job finishes the results are incorporated into the Project Table as a new entry The structure shows the H atom bonded to the O atom with an elongated bond 3 6 Vibrational Frequencies In this exercise you will calculate the vibrational frequencies of the transition state you found in the previous exercise and view an animation of the frequencies in
31. point in the status bar of the main window Click this icon to save the changes and reset your preferences to automatic synchronization Figure 2 2 The completed vinyl alcohol structure Jaguar 7 6 Quick Start Guide 9 Chapter 2 Building Small Molecules In Maestro 10 2 7 Building a Structure by Growing Fragments In this exercise you will use fragments to build a structure as you did in the previous exercise However this time you will build in Grow mode In this mode selected fragments are combined using predefined grow bonds The grow bond is the bond that is replaced when another fragment is selected in Grow mode The fragment is added in an orientation that is determined by the choices made from the Grow direction and Joining geometry option menus 1 Click the Clear Workspace button on the toolbar gt 2 From the Show hide the build toolbar button menu on the toolbar choose Fragments The Build panel is displayed with the Fragments tab on top and the organic fragments library displayed see Figure 2 3 Atom Residue Fragments 9 Properties Properties Define grow bond Place Grow n ii Pick Atoms M Fragments Organic M vesi Kur ai ER pe Van H H whe kn H slolojojo Ae a I H 09 o o o 9 oi i
32. rowse Molecule SCF Solvent Symmetry Use if present Molecular state 7 Use charge and multiplicity from Project Table Create Properties O Use these values Molecular charge jo Spin multiplicity 2S 1 1 O Use pKa atoms from the Project Table Pick to add atoms to Project Table I Perform conformational searches on input structures requires MacroModel job Start Read II Write Edit Reset Close Help Figure 3 12 The Molecule tab for pK calculations 6 Click Start The Start dialog box opens 7 optional In the Job section choose a host from the Host option menu 8 Choose Replace existing entries from the Incorporate option menu 9 Set the job name to pka and click Start The calculation of pK values involves a number of steps and can be time consuming This job takes several minutes to finish The output pK is the only data written to the file methylamine out When the job finishes the pK value is added to the methylamine entry as a property Jaguar 7 6 Quick Start Guide Getting Help Schr dinger software is distributed with documentation in PDF format If the documentation is not installed in SCHRODINGER docs on a computer that you have access to you should install it or ask your system administrator to install it For help installing and setting up licenses for Schr dinger software and instal
33. select Gradient corrected in the Functionals section then choose BLYP from the corresponding option menu You can view the input file contents by clicking the Edit button Notice the addition of keywords in the gen section A BLYP calculation is specified by dftname blyp and a geometry optimization is specified by igeopt 1 Close the panel by clicking Cancel Jaguar 7 6 Quick Start Guide 17 Chapter 3 Running Jaguar Calculations 18 7 Click Start The Start dialog box opens 8 optional In the Job section choose a host from the Host option menu 9 Type benzene dft in the Name text box and click Start The Monitor panel is displayed and shows the job s progress This job takes a few minutes to finish When it has finished close the Monitor panel A new entry named benzene 01 appears in the project table 3 3 Localized MP2 Energy Calculation In this exercise you will determine the MP2 energy of benzene at the DFT geometry 1 Read the restart file benzene dft 01 in as Geometry and settings This file contains the optimized geometry of benzene from the previous exercise See page 16 for instructions about reading files A new project entry is created 2 Choose Applications gt Jaguar gt Single Point Energy in the main window 3 In the Theory tab choose LMP2 local MP2 from the Level of theory option menu Since benzene is aromatic you should use a special form of LMP2 which allows all the elec tron pairs o
34. select the treatment in the Hydrogen Treatment panel which you open from the Edit menu Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro Symmetrize Workspace 2lalx Tolerance 0 04 Find Point Group Point group tolerance 0 04 Cs Symmetrize Figure 2 5 The Symmetrize Workspace dialog box 2 10 Symmetrizing a Structure The molecule you drew is planar but is likely to have no other symmetry In this exercise you will symmetrize the structure so that it has full Dg symmetry then clean up the structure 1 From the Edit menu choose Symmetrize Workspace The Symmetrize Workspace panel is displayed The symmetry is likely to be C The Find Point Group button is dimmed because the structure actually has the symmetry displayed If the point group is not Den increase the tolerance and click Find Point Group until the correct symmetry is located Click Symmetrize The structure takes on the correct symmetry Clean up the structure use the Clean up geometry toolbar button Check in the Symmetrize Workspace panel that the point group symmetry is still Dep If not click Symmetrize This second symmetrization may be necessary because the geometry cleanup perturbs the structure away from its symmetry to ensure that a minimum is found Close the Symmetrize Workspace panel Create a Project Table entry named benzene see Section 2 3 on page 7 Ja
35. space 4 Change the value in the Current column to 0 and press ENTER The dihedral is not adjusted if you do not press ENTER Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro 5 Click the Delete button to remove the defined dihedral from the list The dihedral marker in the Workspace is removed 6 Close the Adjust panel 2 3 Saving Workspace Contents as a Project Entry To model the interconversion between acetaldehyde and vinyl alcohol you will need to convert the acetaldehyde structure to vinyl alcohol Before proceeding save the aldehyde molecule as a Project Table entry This allows you to store the aldehyde structure while you construct the alcohol The Project Table entries are also used to select reactant and product structures for transition state searches and IRC scans 1 Click the Create entry from Workspace button on the main toolbar Ba The Create Entry From VVorkspace dialog box is displayed 2 Type aldehyde in the Title text field and click Create 3 Click the Open Close project table button on the toolbar EH The Project Table panel is displayed with the new entry as the first entry 2 4 Duplicating Project Entries In this exercise you will copy the acetaldehyde entry you have generated to create a new entry for vinyl alcohol 1 In the Project Table panel ensure that the aldehyde entry is selected 2 Type CTRL D A copy of the aldehyde entry is made The new entr
36. st of frequencies and normal modes below the heading start of program freq Below the frequencies is information on the zero point energy entropy and other thermodynamic quantities Vibration vibration Entry 3 trans_state Choose a 2031 212 571 192014 623 569683 765 362144 930 651367 al 1021 5825 Animate Amplitude 1 000000 Slower Faster Speed G 5 Figure 3 10 The Vibration panel Jaguar 7 6 Quick Start Guide Chapter 3 Running Jaguar Calculations 3 7 Intrinsic Reaction Coordinate Calculation In this exercise you will use the results of the transition state search and frequency calculation from the previous exercises to perform an intrinsic reaction coordinate scan and visualize the reaction in Maestro with the ePlayer 1 10 11 12 In the Jaguar panel click Read The Jaguar Read dialog box is displayed Select Geometry and settings from the Read As option menu Read the restart file trans_freq 01 in from the previous exercise The transition state structure is displayed in the Workspace and incorporated into the Project Table The hydrogen atom is located as expected about halfway between its starting and ending position To perform an IRC scan you must read or generate a Hessian In this case the Hessian is read from the restart file trans_freq 01 in In the Project Table click to select th
37. un Jaguar jobs 2 Change to the desired vvorking directory cd directory name 3 Enter the command SSCHRODINGER maestro amp The Maestro main window is displayed and the working directory is Maestro s current working directory Windows e Double click the Maestro icon on the desktop You can also use the Start menu Maestro is in the Schr dinger submenu Jaguar 7 6 Quick Start Guide Chapter 1 Getting Started 1 3 Setting the Maestro Working Directory If you are running Maestro under Windows or if you are using an existing Maestro session under UNIX you must change to the working directory that you created for the tutorial in Section 1 1 1 Choose Change Directory from the Maestro menu 2 Navigate to the appropriate directory and click OK 1 4 Creating a Maestro Project When you start Maestro a scratch project is created This project must be named in order to keep it for later use You should therefore create a named Maestro project to save the structures that you build in case you want to complete the exercises at a later time For more information on Maestro projects see Chapter 8 of the Maestro User Manual 1 Choose Save As from the Project menu The Save Project dialog box is displayed The Look in option menu should contain the current Maestro working directory 2 In the File name text box type JaguarTutorial 3 Click Save This procedure creates a project named JaguarTutorial When you
38. y is automatically selected 3 Click the title of the new entry to edit it 4 Change the title to alcohol and press ENTER 5 Change the entry name of the new entry to alcohol using the same procedure If the entry name is not displayed choose Property gt Show Entry Name Jaguar 7 6 Quick Start Guide Chapter 2 Building Small Molecules In Maestro 2 5 Converting the Acetaldehyde Structure Into Vinyl Alcohol In this exercise you will convert the copy of the acetaldehyde structure into vinyl alcohol by breaking the C H bond changing the bond orders and then connecting the unattached hydrogen to the oxygen atom Converting structures is especially useful for transition state searches when a reactant and a product structure is given because the search relies on a consis tent atom numbering scheme 1 In the Project Table panel click the In box of the alcohol entry The alcohol entry is included in the Workspace and the aldehyde entry is excluded from the Workspace Since the two entries are identical there is no visible change in the Workspace Choose Bonds from the Delete button menu on the toolbar x Inthe Workspace click on the C H bond cis to the C O bond The bond disappears and the H atom is represented by an asterisk Click the Decrement bond order button on the Build toolbar E In the Workspace click on the C O bond The bond should now be represented by a single line indicating a si
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