This menu contains the following commands:
New: Erases current atom data
Open: Read a file
Save: Save the current structure with a specified format.
Save Graphic: Save an image of the screen as Jpeg, Png,or Povray
Print: Print the contents of the current Structure Window.
Recently Opened Files
Exit: Exit Pcmodel
The Open option in the File menu is used to read a new structure file into Pcmodel.
If there is a structure present on the screen you will be prompted to either “Keep” or “Delete” the current structure. Selecting “Keep” allows you to import multiple molecules into the program each of which will have a different molecule number and can be treated separately. This function replaces the Substr Read function in earlier versions of Pcmodel.
Selecting Open brings up a standard 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 remembers the last filetype that was opened and tries to use that when the dialog is reopened. This works on the Macintosh but not on Windows and Linux at the present time due to bugs in the version of Qt. We apologize for the inconvience.
Pcmodel makes no attempt to guess the format of the file you wish to read. A common error is to enter the name of a file but not select a filetype which then results in nothing being displayed on the screen. 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.
SDF and 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. The mol file is a fixed format file and is limited to 999 atoms.
MOL2 files are structure information files developed by Tripos Inc. Mol2 files contain information about atoms and bonds. The input is free format and can contain an unlimited number of atoms. It is our preferred format for large structure files.
XYZ are simple structure files that have only atom information. The basic format starts with a line listing the number of atoms, followed by a line of text for a title and then atom lines with a format of atom symbol and x,y and z cartesian coordinates.
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.
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.
Smiles strings are a linear, 1D, notation for chemical structures. Pcmodel reads the string and attempts to build a 3D structure based solely on the atom types and connectivity.
CML
Gaussian Input (job) Files
Gaussian Log 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.
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.
Mopac AUX
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.
Turbomole files are the output files (text) written by the Turbomole quantum chemistry program. Since Pcmodel reads the text file, the output file is portable across all platforms.
CIF
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.
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 16.)
SDF are structure files generated by the structure building programs Corina and Concord.
MOL2
XYZ
PDB files contain the Cartesian coordinates of the current structure written in PDB format.
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.
Smiles strings are a linear, 1D, notation for chemical structures.
CML
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.
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.
Gamess input files will bring up a dialog box similar to the Gaussian box.
Turbomole files are the input files (text) for the Turbomole quantum chemistry program. Since Pcmodel writes a text file, the file is portable across all platforms.
Lammps
This option saves the screen in one of the following file formats Jpeg, Png, Pdf 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, Linux) at http://www.povray.org.
Print sends the current structure and related information to the default printer (which may be a file). Any information in the structure window (such are queries) will be sent to the printer along with the structure.
This option leaves Pcmodel and returns to the operating system. There are four options: Save the Current Structure in a file, Save the Log file, Exit and Cancel.. Note that any unsaved work will be lost when Pcmodel exits. Older versions of Pcmodel automatically wrote a log file of the calculations called Pcmod.out. In version 10 the log file is written to a temporary directory and will not be saved unless the user specifically asks for it and provides a suitable filename.