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Here are some useful examples of HyperChem script files. If you would like to contribute a script, here is a chance to gain some fame and immortality! (Or possibly notoreity...) Please e-mail the Support Desk with details... support@hyper.com.
REACT.SCR is a script which creates an H+H2 molecular system and then simulates the reaction: H+ + H-H --> H-H + H+
SAVEIR.SCR saves the existing IR spectrum. This script produces or writes over the file "\hyper\chem_ir.scr" which can be run later to recover the IR data. When running chem_ir.scr to regenerate the spectrum you must first have the appropriate molecule in the workspace.
SAVEUV.SCR saves the existing UV spectrum. This script produces or writes over the file "\hyper\chem_uv.scr" which can be run later to recover the UV data. When running chem_uv.scr to regenerate the spectrum you must first have the appropriate molecule in the workspace.
TOR_MM.SCR is a script written by Ron Starkey of the University of Wisconsin-Green Bay in Green Bay, WI 54311. It is a semi-automated script for calculating conformational energies from rotation about a single bond.
The HyperChem script will rotate about a selected torsional angle system from -180 to +180 degrees in 10 degree increments. At each increment the set torsional angle is restrained and an mm+ geometry optimization is performed. The restraint is then removed and an mm+ single point energy is calculated. The 37 single point energy values are sent to a data file named C:\hyper\tor_data.txt. The conformational energy values are in text file format that is suitable for importing to a graphing program or a spreadsheet for graphing. A template for use with Quattro Pro (either version 5.0 or 6.0) is included. This template automates importing and plotting of the data from the tor_data.txt file.
The TOR_MM.SCR script file can be used to easily generate plots of the calculated conformational energies that result from rotation about 1,2-disubstitued ethane systems. The general structural formula for this system would be A-CH2-CH2-B. Butane (1,2-dimethylethane, A=CH3, B=CH3) can be used as a reference standard to evaluate the effective sizes of various groups relative to a methyl.
The QuattroPro template (t_templ.wb1) contains macros that allow importation of the data file (tor_data.txt) with the Ctrl+I keystroke, the substraction of lowest energy value from each conformational energy, and the plotting of the energy values relative to the lowest energy conformation. The graph is found on the second page of the spreadsheet notebook. There is also a printing macro that is activated by Ctrl+P.
With HyperChem, it is easy to construct a periodic box filled with water. This script extends this capability to other solvents as well, by filling a periodic box with non-aqueous solvent. (See HyperChem Newsgroup Archive, March '97.) This script is a sample TCL Script, so it can only be run with HyperChem 5, which supports .TCL-type scripts.
This script will do multiple merges of one file which contains a solvent molecule. It displaces the solvent molecule by a certain amount each time. (This does not do a very fancy placement of molecules.) The TCL script is easily modified to change the number and average displacement of solvent molecules or the identity. Once you have placed as many molecules as you want in the cell, you should do a geometry optimization with a simple potential (e.g. MM+) to distribute the molecules better before doing a molecular dynamics run.
The sample script, "box.tcl" should be placed in the same folder as the sample HyperChem file, "benzene.hin". To run this script, open it from the "Script" menu item in HyperChem 5.
Solvent mixtures in a Box
This script by Yeungee Jin, Sung Kwang Lee and prof. Dai Woon Lee of Yonsei Univ., Seoul, Korea, generates a periodic box filled with different solvents (mixtures) around a solute molecule. This script includes a set of sample molecules and instructions for use.
Here are some very interesting potential uses for this periodic box system:
a) To see solvating effects of various solvent-systems such as liquid chromatography
b) To run molecular dynamics in the mixed solvents' box and for any further purposes you want.
Compatibility: HyperChem Ver. 5.02 (with tcl/tk 7.5) or higher versions. See the included Readme.txt file for details.
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Download REACT.SCR (2 kB)