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 currently release supports the MM3 and MMFF94force 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 currently 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.

 

1.4 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

1.5 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 (QCPE-318), also by N. L. Allinger.  J. McKelvey of Kodak modified the pi-VESCF routines for open shell species, while J. J. Gajewski did improvements to the heat of formation calculations.  MMX increased the number of atom types for the MM2 force field, added the ability to handle transition metals and transition states, and increased the number of parameters included in the database.  J. J. Gajewski and K. E. Gilbert made these changes. 


1.6  The PCMODEL Window

 

            PCMODEL uses a standard window in all versions of the program. The main window in the WindowsTM version is shown below.

 


 

            A menu bar appears at the top of the screen, with 10 options - FILE, EDIT, VIEW, COMPUTE, ANALYZE SUBSTR, TEMPLATES, MARK, OPTIONS, FORCE FIELD and HELP.  The commands under each of these headings are described in detail in later chapters.  A second bar of drawing tools appears along the right hand edge of the screen (this is referred to as the TOOLS menu or Drawtools menu) The Drawtools menu may be moved.  At the bottom of the screen is a status bar, which indicates the status of various options. 

 

1.7  Definitions

 

            Within this manual, the terms window and screen will be used interchangeably to refer to the main graphics window in which PCMODEL is running. 

            The term attached atom refers to an atom with only one connection, such as hydrogen attached to a carbon.  A connected atom is one that is connected to the given atom and may include an attached atom. 

            Pointing, clicking, hitting or pressing a button all refer to a single click of the left mouse button over the word, button, atom or bond. 

            A substructure is a collection of atoms that may or may not be connected, that have a common value among their substructure numbers and an associated name.  Substructures can be moved, rotated, connected, hidden, minimized independently, and docked to one another or to a main structure.  When written with a PCM file format, substructure information is maintained, so substructures can be stored.  A single atom may belong to more than one substructure.  When a substructure is connected to another structure, a bond is formed but the substructure information is maintained.  Thus, a substructure can be part of a contiguous structure, and when the structure is moved or rotated the joining bond can be stretched abnormally.  Remember that, when connecting substructures, the substructure that is chosen many not be the entire connected structure, thus leading to the stretch of one bond in order to form the connected bond. 

 

1.8 Closing Notes

 

            This manual describes only a few of the possible chemical structures that we can study with PCMODEL.  We have tried to do the very best job of representing chemistry with a computer model.  No doubt there are many problems still remaining and many faults with our models.  If you find problems, or think the calculations are incorrect, please let us know.  We are always trying to improve the chemistry of PCMODEL and since we are few and the problems are many, your help is always appreciated.  We can be reached at:

 

Phone               (812)-333-0823

 

FAX                (812)-332-0877

 

Email                gilbert@serenasoft.com

 

WWW             http://www.serenasoft.com/

 

Mail                 Serena Software

Box 3076

Bloomington, IN 47402-3076