Serena Software



PCMODEL Version 9.3 is a complete molecular modeling package for your personal computer or workstation. It is designed and built by research chemists for research chemists to be powerful, versatile and, most of all, easy to use. Within the menu driven structure input mode, PCMODEL allows you to draw structures as you would on paper, substitute, move, and delete atoms, and fix atoms and distances in space. Using a build command you can grow structures with complete control of stereochemistry. The substructure functions allow you to create a library of commonly used substructures to add to your structure in any orientation. Up to 32 named substructures can be created, moved, docked and rotated on screen, all with simple mouse command.

Version 9.3 includes support for different force fields with the MMX, MM3, MMFF94, Amber and Oplsaa force fields currently supported. The computational portion of the code has been completely rewritten which allows the use of more modern minimizers and includes both first and second derivative methods. The conformational searching routines from GMMX have been incorporated to allow for conformational searching on up to four rings and fifty rotatable bonds at one time. Normal vibrational modes may be computed. Various comparison methods are available and the output structures can be queried for distances, angles, dihedrals and coupling constants. The atom limit has been increased to 2500 atoms and support for reading and writing PDB and SDF files has been added.

Pcmodel is an excellent front end for quantum chemistry programs with complete support for Gaussian, Gamess, Jaguar, ADF, PQS, Turbomole, Hondo, Ampac and Mopac. Pcmodel can write standard input files for all of the quantum chemistry programs and options can be setup using simple dialogs. The output of the quantum calculations can be read by Pcmodel and the structural information displayed. Orbital displays and Normal Vibrational modes can be displayed using the auxiliary programs Orbdraw and Vibrate.

Structures may be docked with one or more substructures. Docking can be performed by minimization or by simulated annealing style. A manual docking routine has been added. Specific inter-substructure interactions can be turned on and off so you can minimize only a choosen portion of the substructures. The option of batch minimization for multiple structure files and the choice to minimize individual substructures makes it easy to get the results you want fast.

But how much chemistry does it know? With sixty atom types and generalized parameters, as well as functions and parameters for transition metals, PCMODEL's built-in MMX force field minimizations provide some of the most complete molecular modeling on the market. Unrestricted Hartree-Fock pi calculations for conjugated systems provide unparalleled accuracy for molecular mechanics calculations of open shell species. Standard RHF pi calculation can be used to model closed shell species containing C, N, and O. Also, specific aromatic carbon types provide excellent aromatic geometries without pi calculations. Additionally the MM3, MMFF94, Amber and Oplsaa force fields are included with all the currently published parameters.

Transition metal complexes can be built with explicit sigma bonding, lone-pair coordination and pi-system coordination. Parameters are available for all transition metals. Tests on over 200 structures have shown some classes of compounds to be modeled with better than 0.02* deviation. Now, PCMODEL can treat an unlimited number of metals with up to twenty different metal types per structure.

Hydrogen bonding calculations using angle dependence as well as distance dependence is included explicitly in the MMX force field. Specific hydrogens can be marked as participating in hydrogen bonding or not. Transition state modeling and dynamics simulations are incorporated into PCMODEL and reachable with just the press of a button.

If PCMODEL still doesn't have parameters you need, you can add your own constants as easily as editing a file. You can add bond angles, bond lengths, torsion constants and dipole information by creating an easily readable constants file. Display options in PCMODEL work to complement the advanced calculations in giving you the information you need from molecular modeling. Charge surfaces, solid Van der Waals surfaces, water solvation surfaces are all displayed on the screen or they can be sent to a printer or plotter. Graphical polypeptide backbone ribbons and Ramachandran plots provide the tools to make PCMODEL useful to biochemists and educators in a large number of applications.

Geometry and charge parameters are easily obtainable on screen; distances, angles, torsional angles, vicinal H-H coupling constants and the atomic charge are displayed just by pointing. Structure comparisons list complete difference information between two structures and allow overlapping structure display.

PCMODEL also reads and writes files for many other types of molecular calculation programs including MM2, MM3, MOPAC, Ampac, Gaussian, Gamess, Jaguar, Hondo, TurboMole, Macromodel, Alchemy, Sybyl,Chem-3D, PDB and SDF so you can create and edit your preferred structure calculation files. Alternatively, you can use the PCM file format, an easily readable, free-format file that maintains all structure information including substructure names and membership, atomic charge, and user-specified minimization parameters. Since these files are ASCII text files, they can be transferred to another computer as input to calculations on another system.

PCMODEL documentation provides tutorials which give step by step examples of the use of the major functions, as well as detailed descriptions of each button, file structure, menus and the force field.

PCMODEL version 9.3 is available for :

  • Windows XP, 2K, and 7
  • MacOS X

Price $600 list, $400 academic, updates $200 for Windows, Linux, Mac and Unix Workstations.

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        Tel:   (812)-340-1143

Last updated: 3/21/11 "Kevin E. Gilbert"
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