Parameter file

Select Setup/Compile Parameter File to create a new binary ,par parameter file that includes the new type. 

Hor the 6 l2l alrVDWFurmaL entry set to AijHlj, the values in the parameter file are not converted. 

The entries in molecular mechanics parameter files are described in th e /lypcrChem iicfcre.nce Manual. Tfse th e folio won g proced ii re to modify an existing parameter set ... 

The correcnoii is only applietl in the del ank MM+ paraincier scheine. When MM+ pnranieiers are available in the inmp-sLr.txUtlbf) lile, the normal approach based on only atom types is used. Thus, the correction is applied Lo butadiene when all the atom types are, for example, but not when atom types are present and their corresponding parameters available in the parameter files. 

Enter Cartesian Coordinate Eile Name cbu2.xyz Enter Potential Parameter File Name mm3... 

A diva It MM3 wilh Ihe cumrnand mm3. Answer questions file etheiie.mm3, parameter file Enter (default) line number 1, option 2. The defaull parameter sel is Ihe MM3 parameler sel don t ehange il. The line number starts Ihe system reading on the first line of your input file, and option 2 is the block diagonal followed by full matrix minimi7 ation mentioned at the end of the section on the Hessian matrix. You will see intermediate atomic coordinates as the system minimises the geometry, followed by a final steiic eireigy, Kird with 0, output Enter, cooidinates Enter,... 

The HyperChem MMh- code and program also differ from MM2(1977) by having parameters in text files separate from the code. These parameter files are available for your modification and additions. The parameters distributed with HyperChem include the public domain values, generally referred to as the MM2(1991) parameter set, that Dr. Allinger contributed to HyperCube, Inc. Parameters not obtained from Dr. Allinger are appropriately labeled in the distributed parameter files. 

The new parameter files must be compiled for each parameter set used with the particular force field that has the new type, as follows ... 

The force fields in HyperChem that use the above 6-12 potential allow six ways of specifying the constants Ay and B.. three by single atom type and three by pairs of atom types. Single atom type means that there are constants for individual atom types, i, that are combined by a combining rule that results in a parameters for a specific pair, ij, of atom types. Pairs of atom types means that parameter files contain explicit parameters for a pair of atom types... 

Two Tq values are given for each MM+ bond, and rg . If rg is available (has a non-zero value in the parameter file) then it is used in preference to the normal for bonds where atom i and atom j have at least two hydrogen atoms directly attached to them. For example, CH2-CH2, CH2-CH3, or CH3-CH3 bonds may have their own equilibrium distance differentiated from the average single bond between carbon atoms. 

The text form for parameters uses white space or commas to separate the fields (columns) of the parameter files. They can be read by ordinary text editors, word processors, etc. In the text form, parameters are easy to modify but not easy to compare, study, etc. Many database programs are capable of reading columns of text as a database, however. While spreadsheets are not, per se, databases, they can be useful for examining parameter sets. Microsoft Excel, for example, can read the text form of a parameter file and put the data in a form easily manipulated as a matrix or a database. The text form of parameters are stored, by default only, in. txt files. 

Compilation of parameters makes HyperChem more efficient. It replaces a set of text or dBASE files (for one parameter set) by a single binary. par file. The compilation can be performed at any time from within HyperChem by selecting the parameter set (Setup/Select Parameter Set) and requesting a compilation (Setup/Compile Parameters). If the parameter files are not modified, you do not have to compile them. 

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