Chapter 6. File Menu

 

            This menu contains the following commands:

 

Open                           Reads a file containing a molecular system

Save                            Writes a molecular system to a file

Save Graphic              Writes a file containing a picture of the screen

Print                            Print the current molecular system

Read pcmod.bak        Read the structure backup file

Exit                             Exit PCMODEL

 

6.1 Open

 

            The OPEN option in the FILE menu is used to read a new structure file into PCMODEL.  Any structure on the screen will be erased.

 

           

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Macintosh: Selecting OPEN immediately brings up a standard Macintosh file open dialog box with the different file formats listed in a drop down window at the bottom of the dialog box.

 

            Windows and Linux: Selecting OPEN immediately brings up a standard Windows Open File dialog box which gives the current path, an edit window for the filename, a drop down box containing the various file types supported by PCMODEL, a window listing directories and disk drives, and a scrollable window listing the files in the current path (if a wildcard expression is used for the filename).  When the dialog box first appears, the PCMODEL file type is selected and all files with the .pcm file extension will be shown.  A filename may be entered by typing the name in the filename edit box or by selecting (with the mouse) a file from the scrollable file list box.  To see files available in the current path, use a wildcard expression such as *.PCM to see all files with the PCM extension, or *.* to see all files. 

 

            PCMODEL supports several different types of files.  Clicking on the combo box at the bottom of the dialog box will show all the types of files that can be read in PCMODEL.  The default file type is PCMODEL.

File Types Read by PCMODEL

 

PCMODEL files contain information about all the atoms and bonds in a molecule, including information about hydrogen bonding, pi atoms, metal coordination and substructure membership.  It is the most general file type for molecular mechanics information, is a free format ASCII text file, and can be read or edited with any word processor. A PCMODEL file can contain either one structure or multiple structures.  PCMODEL files can be read by Gaussian 92 and can serve as input to this ab initio quantum chemistry program.  (A full description of this file type is given in chapter 6.)

 

MMX files are essentially MMP2 formatted files (see QCPE program number 395 for a detailed description).  These files contain information about atoms and bonds in a molecule, including information about pi atoms, hydrogen bonding and metal coordination, but not substructure membership.  An MMX file can contain either one substructure or multiple substructures.  It is an ASCII text file with a fixed, Fortran format, and can be read or edited with any word processor.  The fact that it is fixed format means that data must be entered in specific columns to be read correctly, which makes editing difficult.  (A full description of this file type is given in chapter 6.)

 

MM3 files contain information about all the atoms and bonds in a molecule written in the MM3 format and using MM3 atom type rules. MM3 files are text files and use a Fortran type fixed format. The files may be edited with a text processor, but the fixed format requires that data be entered in specific columns to be read correctly.

 

PDB files are structure files using the Protein Data Bank format developed at Brookhaven National Laboratory. The PDB format can be used to describe any molecule and is not restricted to proteins or nucleic acids. The PDB format contains information about the atom type, the residue name if part of a protein or nucleic acid, and the atomic coordinates of the atom. Bonding information may be included in the file but it is not required. PCMODEL reads PDB files and tries to determine the bonding arrangement based on internuclear distances. While this method is good it is not perfect and the bonds shown when a PDB file is read should be looked at carefully before further calculations are attempted.

 

MOPAC INP and ARChive files are used by the semi-empirical quantum chemistry programs, AMPAC and MOPAC (QCPE program number 514).  These files contain a list of atom symbols, bond lengths, angles and dihedral angles, but no information about bonding. MOPAC files may be used for input to the AMPAC, MOPAC and Gaussian programs since all of these programs can read and interpret internal coordinates. The INP file is an input file to AMPAC or MOPAC in Z matrix format and the ARChive file is the archive output file written by Mopac (normally FOR012) and contains the optimized geometry in Z matrix form and the atomic charges calculated by Mopac. Both the structure and charges can be read into PCMODEL.

 

Alchemy and Sybyl molecular modeling programs marketed by Tripos Associates (St. Louis, MO) use ALCHEMY and SYBYL files.  Alchemy file format is also used by Chemical Abstracts Service for 3D-structure information. 

 

MACROMODEL files are molecular mechanics type files generated by the Macromodel program.  This large molecule modeling program, developed by C. Still, Columbia University, runs on workstations and provides many facilities for handling large molecules.  Macromodel files contain information about atoms and bonds, but no information about pi atoms, hydrogen bonding or transition metals. 

 

X-RAY files are free format structure files in a format that has been developed for reading x-ray crystal data.  X-ray structure files only contain information about atom types and positions.  (A full description of this file type is given in chapter 6.)

 

CHEM-3D is a molecular modeling program developed by Cambridge Scientific Software for use on a Macintosh computer.  PCMODEL reads and writes the Cartesian type II structures. Chem-3D can be used to generate publication ball and stick pictures. 

 

TINKER is a molecular modeling program developed by Professor Jay Ponder of Washington University (ponder@dasher.wustl.edu). PCMODEL reads and writes the xyz cartesian filetype.

 

MDL_MOL files are structure information files in the molfile format developed by MDL Information Systems Inc. Molfiles can be generated by programs such as Isis™ Draw, or as the result of a search of the REACCS or MACCS databases. Molfiles contain 3-D structure and bonding information.

 

Corina and Concord are structure files generated by the structure building programs Corina and Concord.

 

Gaussian files are the output files (text) written by the Gaussian Quantum Chemistry programs running under Windows, on a workstation or supercomputer.  Since PCMODEL reads the text file, the output file is portable across all these platforms.

 

Gaussian ChkPt files are the formatted checkpoint files generated by the Formchk utility of the Gaussian program.

 

Jaguar Input and Log files are input and output files written by the Jaguar quantum chemistry program from Schrodinger, Inc.

 

CSSTR files are Cambridge Structural Database files.

 

Gamess files are the output files (text) written by the Gamess Quantum Chemistry programs running under Windows, Macintosh, on a workstation or supercomputer.  Since PCMODEL reads the text file, the output file is portable across all these platforms.

 

Hondo files are the output files (text) written by the Hondo Quantum Chemistry program.  Since PCMODEL reads the text file, the output file is portable across all platforms.

 

 

6.2 Save

            The SAVE option is used to write the current molecular system to a disk file. 

 

            Macintosh: Selecting Save brings up a dialog box listing the current types of files PCMODEL can write. Select the appropriate file format and then OK. The standard Macintosh file save dialog box will then be presented.

 

            Windows and Linux: Selecting SAVE brings up a standard Windows File Save dialog box which gives the current path, an edit window for the filename, a list box containing the various file types supported by PCMODEL, a window listing directories and disk drives, and a scrollable window listing the files in the current path (if a wildcard expression is used for the filename).   All files with the default extension will be shown.  The last file name used will be retained.  If this file is used again, you will be asked if you want to replace the file or append the structure onto the existing file.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

When the dialog box first appears, a wildcard expression is displayed in the filename edit box, and the PCMODEL file type is selected.  All files that match the wildcard expression will be listed in the file list box.  A filename may be entered by typing the name in the filename edit box or by selecting (with the mouse) a file from the scrollable file list box.  To see files available in the current path, use a wildcard expression such as *.PCM to see all files with the PCM extension, or *.* to see all files. 

            If the filename that is entered already exists, a dialog box will appear asking if the new structure is to be appended to the existing file, or if the existing file is to be replaced.  Choosing APPEND to generate multiple structure files or libraries of related structures. 

            The current directory is given in the current path box.  The directory list box displays all directories below the current directory, the directory one level up from the current directory ([..]), and all other disk drives on the computer.  The current path may be changed by selecting either another directory or disk drive in the directory list box. 

            PCMODEL supports several different types of files.  Clicking on the combo box at the bottom of the dialog box leads to a drop down menu of all the files written by PCMODEL.  The default file type is PCMODEL. MMX atom types are assumed for all files except MM3 files where the MM3 atom types are assumed.

 

File Types Written by PCMODEL

 

PCMODEL files contain information about all the atoms and bonds in a molecule, including information about hydrogen bonding, pi atoms, metal coordination and substructure membership.  It is the most general file type for molecular mechanics information, is a free format ASCII text file, and can be read or edited with any word processor. A PCMODEL file can contain either one structure or multiple structures.  PCMODEL files can be read by Gaussian 92 and can serve as input to this ab initio quantum chemistry program.  (A full description of this file type is given in chapter 6.)

 

MMX files are essentially MMP2 formatted files (see QCPE program number 395 for a detailed description).  These files contain information about atoms and bonds in a molecule, including information about pi atoms, hydrogen bonding and metal coordination, but not substructure membership.  An MMX file can contain either one substructure or multiple substructures.  It is an ASCII text file with a fixed, Fortran format, and can be read or edited with any word processor.  The fact that it is fixed format means that data must be entered in specific columns to be read correctly, which makes editing difficult.  (A full description of this file type is given in chapter 6.)

 

MM3 files contain information about all the atoms and bonds in the molecule. The MM3 atom types are used and pi atom marking is supported.

 

MOPAC and AMPAC files are used by the semi-empirical quantum chemistry programs, AMPAC and MOPAC (QCPE program number 514).  These files contain a list of atom symbols, bond lengths, angles and dihedral angles, but no information about bonding.  MOPAC files may be used for input to the AMPAC, MOPAC and Gaussian programs.  The dialog box will facilitate writing the file.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ALCHEMY and SYBYL files are used by the Alchemy and Sybyl molecular modeling programs, marketed by Tripos Associates (St. Louis, MO).  Alchemy format is also used by Chemical Abstracts Service for 3D structure information. 

 

MACROMODEL files are molecular mechanics type files generated by the Macromodel program.  This large molecule modeling program, developed by C. Still, Columbia University, runs on workstations and provides many facilities for handling large molecules.  Macromodel files contain information about atoms and bonds, but no information about pi atoms, hydrogen bonding or transition metals. 

 

CHEM-3D is a molecular modeling program developed by Cambridge Scientific Software for use on a Macintosh computer.  Chem-3D can be used to generate publication ball and stick pictures. 

 

Tinker is a molecular modeling program developed by Professor Jay Ponder of Washington University in St Louis. PCMODEL generates an  xyz cartesian file that can be read by Tinker.

 

PDB files contain the Cartesian coordinates of the current structure written in PDB format.

 

Jaguar Input files are written for the Jaguar quantum chemistry program. They include the Cartesian coordinates of the structure and the atomic symbol.

 

Gaussian Job files are input files for the Gaussian quantum chemistry program.  Structural information can be output in either Cartesian or Z matrix format and many options may be set using the dialog box.  The Keywords section is updated each time an option is selected. If you wish to add additional keywords not available through the options, they should be added just before OK is selected.

 

Gamess input files will bring up a dialog box similar to the Gaussian box.

 

Hondo input files will bring up a dialog box similar to the Gaussian box.

 

Corina and Concord are structure files generated by the structure building programs Corina and Concord.

 

6.3 Save Graphic

 

            This option saves the screen in one of the following file formats; GIF, BMP, HPGL, PostScript or POVRAY.  The file may then be imported into other programs for editing.  The POVRAY option will write a file for input into the rendering program POVRAY.  This program is freely available for a number of platforms (PC, Mac, UNIX) at http://www.povray.org.  It will provide a ray-traced picture of the molecule as shown to the left for potassium 18-crown-6.

 

 

 

 

 

 

 

 

 

 

6.4 Print

 

            Print sends the current structure and related information to the default Windows printer (which may be a file).  The Print Manager handles printer selection in WindowsTM or by the Chooser on the Macintosh.  When PRINT is selected, a dialog box appears containing the currently selected printer. If the current structure is drawn as a stick figure then a dialog box will be shown  with options for printing the current structure and compare or energy windows. If the current structure is drawn in Ball and Stick, Tubes or CPK modes then the second dialog box will not be shown and the output and compare windows will not be printed.  Any information in the structure window (such are queries) will be sent to the printer along with the structure.

 

6.5 Read pcmod.bak

 

            Every time a minimization is started and upon its completion a structure file, pcmod.bak, is written to the current working directory.  This option will read in this file.

 

6.6 Exit

 

            This option leaves PCMODEL and returns to the operating system.  A dialog box asks for confirmation before exiting.  Note that any unsaved work will be lost when PCMODEL is exited.