HOW TO GENERATE ZMATRIX FOR MCPRO HOW TO

Torsional parameters are typically assigned based on atom classes. The second part of this file contains torsional parameters. For examples, both atom types 135 and 157 belong to the class of tetrahedral carbons (CT) but these two atoms carry different partial charges because type 135 is for the terminal methyl group while type 157 is for the methylene next to the oxygen. It also establishes connection between numerical atom types and letter-coded atom classes. The first part defines nonbonded parameters-charge, sigma, and epsilon- for each atom type. You can inspect this file by typing more etoh_oplsaa.par into the UNIX shell. For the purpose of the tutorial, a simplified copy of parameter file is provided by retaining only the parameters needed to simulate ethanol in water. Inspect the nonbonded and torsional parameter file. Because BOSS is written in Fortran, the position of fields in the parameter file should be kept as is. The optional last column is for comments. The first column defines the bonds and angles by atom classes, the second column gives the harmonic force constant and the third column gives the reference bond length or angle values. You can inspect this file by typing more etoh_oplsaa.sb into the UNIX shell. For the purpose of the tutorial, a simplified copy of the parameter file is provided by retaining only the parameters needed to describe ethanol. Inspect the bond stretching and angle bending parameter file. BOSS z-matrices can be generated from other coordinate files using the program autozmat. MOLDEN provides a graphical interface that facilitates construction of z-matrices.

HOW TO GENERATE ZMATRIX FOR MCPRO HOW TO

The z-matrix is a very important concept in computational chemistry and you need to understand how to construct z-matrices.

For example, the sixth atom (C of CH3, atom type 135) is connected to the fifth atom (C of CH2, atom type 157) by a bond that is 1.53 Ang long, forms an angle of 108.9° with the first atom (O, atom type 154) and forms a torsional angle of 180° with the fourth atom (H, atom type 155). The Z-matrix format defines the structure via connectivity of atoms using the distance, angle, and torsion. The molecular structure is described in the Z-matrix format. Inspect the structure file, named here etoh.z. Change into this subdirectory and verify that you have eight files. etoh should create subdirectory etoh and copy the needed files. Job command file (shell script to launch the job)Ĭopy the files that you need for following the tutorial into a subdirectory in your directory.Job control file (generated by the program pargen).Nonbonded and torsional parameter file (oplsaa.par).Bond stretching and angle bending parameter file (oplsaa.sb).

Structure file for the solute (molecule.z).

It currently lacks a graphical user interface but the results of calculations can be easily visualized using standard molecular visualization (e.g. Ethanol in Water: BOSS TutorialīOSS is a complex program that uses several text files for input. The following tutorial illustrates how BOSS can be used to learn about the structure of ethanol in aqueous solution. Jorgensen's group at Yale University is currently using this program to study solvent effects on organic reactions a closely related program MCPRO is used for rational design of novel inhibitors for important drug targets, such as HIV reverse transcriptase. Bill Jorgensen and his group members over the last few decades. One versatile program that implements Monte Carlo molecular simulations is BOSS, written by Prof. The Monte Carlo method provides one way to perform simulations of dissolved molecules. In essence, molecular simulations allow estimation of properties of neat liquids and solutions by averaging over a large number of solution configurations that are sampled according to the Boltzmann distribution. The set of methods that allow computational study of molecules at real temperatures in solutions is known as 'molecular simulations'. Most interesting chemistry, however, happens at much warmer temperatures and in solutions. The minimum energy structures found during the conformational analysis represent structures that the molecule adopts at 0 K in the gas phase. Monte Carlo Simulations of Solutions and Liquids Molecular Simulations

Practical Monte Carlo Tutorial: Solute Structure in Solution

How to generate zmatrix for mcpro