Pcmodel V 9.0

PCMODEL V 9.0

Molecular Modeling Software

for

Windows Operating System

Apple Macintosh OS

Linux and Unix

First Edition June 1998 Second Edition June 1999 Third Edition January 2001 Fourth Edition April 2002 Fifth Edition August 2003 Sixth Edition August 2004

Trademarks

IBM and IBM PC are registered trademarks of International Business Machines Inc. Windows is a registered trademark of the Microsoft Corporation. Alchemy and Sybyl are registered trademarks of Tripos Associates, Inc. Chem-3D is a registered trademark of Cambridge Scientific Computing, Inc. ISIS is a trademark of MDL Information Systems, Inc.

2 License Agreement

Serena Software provides these programs and licenses their use in your teaching and research. You assume responsibility for the use of the program to achieve your intended results.

You may: 1. Use the programs on any machine or machines in your possession. 2. Copy the programs and source code into any machine readable form for backup or modification purposes in support of your use of the programs. 3. Modify the programs and source code or merge them into another program for your use. (Any portion of these programs or source code or merged programs resulting will continue to be subject to the terms and conditions of this agreement.)

You may not: 1. Give copies of these programs to anyone else, unless you destroy all copies you have in any form. 2. Sell copies of these programs. 3. Use the programs on a network, unless others are prevented from accessing the programs.

This license is effective until terminated. You may terminate it at any time by destroying the programs and source code together with all copies, modifications and merged portions in any form. These programs are provided "AS IS" and without warranty of any kind, either expressed or implied. The entire risk as to the quality and performance of the programs is with the user. Serena Software does not warrant the operation of the programs will be uninterrupted or error free. If Serena Software is unable to deliver a copy of the programs that is satisfactory, you may obtain a full refund by returning all the program materials and documentation within 30 days of date of delivery. These programs are intended for use in chemical research and teaching. Serena Software will not be liable in any event to you for any damages, including any lost profits, lost savings or other incidental or consequential damages arising out of the use or inability to use these programs even if Serena Software has been advised of the possibility of such damages, or for claim by any other party.

3 Table of Contents Table of Contents ...... 4 Chapter 1. Overview...... 9 1.1 Introduction ...... 9 1.2 Changes in Version 7...... 9 1.3 Changes in Version 7.5 ...... 9 1.40 Changes in Version 8.0 ...... 10 1.41 Changes in Version 8.5 ...... 10 1.42 Changes in Version 9.0 ...... 10 1.5 History...... 10 1.6 The PCMODEL Window...... 12 1.7 Definitions...... 13 1.8 Closing Notes ...... 13 Chapter 2. Installation...... 15 2.1 Windows Installation ...... 15 2.2 Macintosh Installation...... 15 2.3 Linux Installation...... 16 2.4 General Comments ...... 17 Chapter 3. Quick Summary of PCMODEL Menu Bar Functions ...... 19 Chapter 4. Tutorials...... 25 4.1 Methylcyclohexane...... 25 4.1.1 Drawing the Structure ...... 25 4.1.2 Building the Structure ...... 28 4.1.3 Minimizing and Adjusting the Structure...... 29 4.2 Trans-Decalin ...... 30 4.3 Special Options...... 31 4.3.1 Compare ...... 31 4.3.2 Rotational Energy Barriers ...... 32 4.4 Benzene and a Pi Calculation...... 32 4.5 Biphenyl and a Pi Calculation ...... 32 4.6 Ferrocene - Using Metals and Coordination ...... 33 4.7 The Methanol dimer - Hydrogen Bonding and Docking ...... 33 4.8 Substructures - Creation and Manipulation...... 34 4.8.1 Building Polystryene using Dummy Atoms...... 35 4.9 Diels-Alder Transition State...... 35 Chapter 5. Drawing Tools...... 38 5.1.1 Select Atom ...... 38 5.1.2 Select Bond...... 38 5.2 Draw...... 38 5.3 Build...... 39 5.4 Update ...... 39 5.5 H/AD...... 39 5.6 Add_B ...... 39 5.7 In ...... 39 5.8 Out ...... 39 5.9 Del...... 40 5.10 Move ...... 40 5.11 Rotate Bond...... 40 5.12 Query...... 40 5.13 PT...... 41 5.14 Metals...... 41 5.15 Rings ...... 42 5.16 AA...... 42 5.17 Su ...... 42

4 5.18 Nu...... 43 5.18 Organo Metallics Templates...... 43 5.20 Transition State Templates...... 44 Chapter 6. Conformational Searching ...... 46 6.1 Setup Rings...... 47 6.2 Setup Bonds...... 48 6.3 Setup Query...... 48 6.4 Comparison Method...... 49 6.5 Options ...... 50 6.6 Run GMMX ...... 50 6.7 Run 2nd Cycle...... 51 6.8 Save Job ...... 51 6.9 Read Job ...... 51 Chapter 7. File Menu...... 53 7.1 Open...... 53 7.2 Save...... 56 7.3 Save Graphic ...... 60 7.4 Save Movie...... 60 7.5 Print...... 60 7.6 Read pcmod.bak ...... 61 7.7 Exit...... 61 Chapter 8 Edit Menu ...... 63 8.1 Draw...... 63 8.2 Erase...... 64 8.3 Structure name...... 64 8.4 Hide Hydrogens...... 64 8.5 Epimer...... 64 8.6 Enatiomer ...... 64 8.7 Remove LP...... 64 8.8 Retype ...... 64 8.9 Set Atom Type...... 65 8.10 List Atom Types ...... 65 8.11 Read Pcmod.out...... 65 8.12 Read Pcmod.err...... 65 8.13 Copy_To_Clipboard ...... 65 8.14 Orient_XY Plane ...... 65 8.15 Build Solvent Box/Solvate ...... 65 8.16 Build Periodic Box...... 66 Chapter 9 View Menu...... 69 9.1 Control Panel...... 69 9.2 Labels...... 70 9.3 Mono/Stereo ...... 71 9.4 Stick Figure ...... 71 9.5 Ball and Stick ...... 71 9.6 Pluto ...... 71 9.7 Tubes...... 71 9.8 CPK_Surface ...... 71 9.9 Dot_Surface...... 72 9.10 Ribbon...... 72 9.11 Red/Green Stereo...... 72 9.12 Top View...... 72 9.13 Dipole Vector ...... 72 Chapter 10 Compute and Force Field Menus ...... 74 10.1 Minimize ...... 75 10.2 Single Point ...... 76 10.3 Use External Charges...... 76

5 10.4 Use Gasteiger Charges ...... 76 10.5 Normal Vibrational Modes...... 76 10.6 Mopac...... 76 10.7 Ampac ...... 77 10.8 Gaussian ...... 77 10.9 Gamess ...... 77 10.10 Orbitals...... 78 10.11 Vibrations ...... 78 10.12 GMMX...... 78 10.13 Metropolis-MC ...... 78 10.14 Vibrational Mode Search...... 78 10.15 Dynam ...... 79 10.16 Auto Dock ...... 79 10.17 Manual Dock ...... 80 10.18 Batch ...... 81 10.19 Rot_E...... 81 10.20 Dihedral Driver...... 82 10.21 Relaxed Grid Search ...... 83 Chapter 11 Analyze Menu ...... 85 11.1 Surface Area ...... 85 11.2 Volume...... 85 11.3 Connolly Surface ...... 85 11.4 Compare ...... 85 11.5 Dihedral Map...... 87 11.6 Movie ...... 87 11.7 Dot Map...... 87 11.8 MultiStructure...... 88 11.9 Assign Symmetry...... 89 Chapter 12 Substr Menu ...... 91 12.1 Read ...... 91 12.2 Create ...... 91 12.3 Move ...... 91 12.4 Connect ...... 92 12.5 Fuse ...... 92 12.6 Erase...... 92 12.7 Show Dummy...... 92 12.8 Don't Minimize...... 93 Chapter 13 Mark Menu...... 95 13.1 H_Bonds...... 95 13.2 Pi Atoms...... 95 13.3 Metal Coordination ...... 96 13.4 TS_Bond Orders ...... 96 13.5 Fix_Distances ...... 96 13.6 Fix Angle...... 97 13.7 Fix_Torsions...... 97 13.8 Reset...... 97 Chapter 14 Options Menu...... 99 14.1 Printout...... 99 14.2 Dielc...... 99 14.3 DPDP ...... 99 14.4 Minimizer ...... 100 14.5 MMX_PI Calculation Options...... 100 14.6 Added Constants...... 101 14.7 Standard Constants...... 101 14.8 Stereo ...... 101 14.9 Pluto ...... 101

6 14.10 Vdw Surface ...... 102 14.11 Dot Surface...... 102 15 The MMX Force Field...... 105 15.1 The MMX Force Field ...... 105 15.2 Minimization with PCMODEL (hints) ...... 107 15.3 Transition State Atoms...... 108 15.4 Pi Calculations...... 109 15.4.1 Pi Atoms ...... 109 15.4.2 Heat of Formation of Pi Systems ...... 110 15.5 Transition Metals ...... 111 Chapter 16 File Formats ...... 114 16.1 PCM File Format ...... 114 16.2 MMX Input Files ...... 119 16.3 Mopac and Ampac Files...... 135 16.4 X-RAY Files...... 136 16.5 SDF and Mdl Mol Files...... 137 16.6 Chem3D and Tinker Files ...... 137 16.7 Cambridge Structural Database Files...... 137 16.8 Alchemy and Sybyl Mol Files...... 137 16.9 Gaussian Input and Output Files...... 137 16.10 Gamess Input and Output Files...... 137 16.11 ADF, PQS, Hondo and Turbomole Files ...... 137 16.12 Smiles Files ...... 137 Chapter 17 Parameter Files...... 138 17.1 Overview ...... 138 17.2 Atom Types ...... 139 17.3 Bonds ...... 139 17.4 Angles ...... 140 17.5 Stretch-Bend...... 141 17.6 Torsions...... 141 17.7 Van der Waals ...... 142 17.8 Charge and Dipole ...... 142 17.9 MM3 Specific...... 142 17.10 Pi Calculations...... 143

7 8 Chapter 1. Overview

1.1 Introduction

PCMODEL is an interactive molecular modeling program for the study of organic and inorganic molecules. PCMODEL is simple to use and has a number of structure creation, display and energy minimization options. In this manual, we will discuss installation of the program, the features of the various menus, the different force fields supported by PCMODEL, and the formats of the various files that can be read and written. A short tutorial on structure building and manipulation is also included. A complete discussion of the methods of molecular mechanics is beyond the scope of this manual. General information about molecular mechanics can be found in the book "Molecular Mechanics", U. Burkert and N. L. Allinger, ACS Monograph Series, Number 175 and in "A Handbook of Computational Chemistry: A Practical Guide to Chemical Structure and Energy Calculations", by Tim Clark, J. Wiley and Sons, 1985. More current information can be found in "Journal of Computational Chemistry", edited by N. L. Allinger and the book series "Reviews in Computational Chemistry", edited by K. Lipkowitz and D. B. Boyd.

1.2 Changes in Version 7

Version 7 of PCMODEL introduces several major changes; the most important of which is the addition of support for other force fields. The current release supports the MM3 and MMFF94 force fields in addition to the MMX force field that was in earlier versions of PCMODEL. Planned for future releases is support for the Amber, Charmm and OPLS force fields. In order to support additional force fields we have rewritten the entire force field section of the code, added new minimizers and changed the format of the parameter files. Version 7 includes both a first derivative minimizer and also a full-matrix second-derivative minimizer.

1.3 Changes in Version 7.5

Version 7.5 of PCMODEL introduces several additional changes. The current release now supports the AMBER force field. Additional items have been added to the Menu Bar. Some items under the View and Compute options have been moved to a new Analyze menu item. The View options now include the ability to change the screen background color, to view structures in red and green stereo, to have a small top view of the structure and to display a dipole vector. The Analyze menu options have added the ability to display the molecular symmetry, and view/analyze multiple structure files. With the multiple structure option one may view in sequential or random order a multiple structure file. One may also do a query on a set of structures, extract structures which match a query or do a global comparison of all structures in a file. The Compute menu option has added the ability to do normal vibration mode calculations and the ability to do conformational searches using low-mode vibrations. The use of solvents has also been improved. 1.40 Changes in Version 8.0

Version 8.0 of PCMODEL includes support for the Oplsaa force field, reading Gaussian Formatted checkpoint files, reading and writing Hondo files. In the Compute Menu there are options to use charges read from a structure file or Gasteiger charges rather than the default force field charges. There is a Manual Docking option, and there are more options for running Batch calculations. The ability to change the atom colors and the background colors has been added to the Options Menu

1.41 Changes in Version 8.5

Version 8.5 of PCMODEL adds support for the PQS, ADF and Turbomol quantum chemistry programs. In the File Menu there is now an option to save Movie files, under the Save Graphics option there is support for PovRay files. In the Edit Menu there is support for reading the Pcmod.Err and Pcmod.Out files so that errors due to missing constants can be checked without exiting PCMODEL. In the View Menu there is an option to show the Backbone of a polypeptide and in the Compute Menu an option for a Relaxed Grid Search. In the Analyze Menu there is an option for calculating surface areas and volumes using the Connolly algorithms, and there is further support for analyzing multiple structure files. The Templates Menu now contains a set of Heterocycles and the Substr Menu now has a Fuse option for fusing two rings.

1.42 Changes in Version 9.0

Version 9.0 of PCMODEL has a completely rewritten graphics engine based on OpenGL. This greatly improves rendering of screen images. Highlighting of atoms or bonds is now visible in Stick Figure, Ball and Stick and CPK views. The format of the ouput window has been changed. The Movie option now reads Gaussian 03 formatted checkpoint files for IRC calculations. Two dimensional SDF files, such as those output by Isis Draw, that contain stereochemical information can now be converted to three dimensional structures. In the Edit Menu there is now an option to Set the atom type of a specific atom, and also an option to List all the atom types in the current force field. In the Options menu the user can now reset the paths which point to external programs such as Gaussian, Gamess or Mopac.

1.5 History

PCMODEL is derived from several sources. The graphical user interface originally came from MODEL, written by C. Still. It has been extensively modified for PCMODEL for WindowsTM. MODEL was ported to the IBM-PC and renamed PCMODEL by M. Mark Midland, University of California, Riverside, J.J. Gajewski of Indiana University, Kosta Steliou of Boston University and K.E. Gilbert of Serena Software. K. E. Gilbert, J. J. Gajewski and T.W. Kreek of Indiana University then ported PCMODEL to the Macintosh, Silicon Graphics and Sun workstations. K.E. Gilbert wrote the current version of PCMODEL for Windows, the Apple Macintosh, Unix and Linux.

The default force field used in PCMODEL is called MMX and is derived from MM2 (QCPE-395, 1977) force field of N. L. Allinger, with the pi-VESCF routines taken from MMP1