In this page you will find information regarding the softwares created in our group and how to get those. The softwares currently being developed by our group are:
- MOLARIS
- CHEMSOL and CHEMSOL ON-LINE
- QCFF/SOL
- MOLARIS_PKA
MOLARIS includes our powerful programs POLARIS and ENZYMIX in
a unique package with an extremely improved interface and maximum robustness.
MOLARIS incorporates the methodologies of the old packages ENZYMIX and POLARIS
and also the more recent advances developed in our group:
- ENZYMIX is a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method.
- POLARIS is a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach, it is used for the calculation of free energies and electrostactic properties of molecules and macromolecules in solution through the evaluation of the permanent dipoles, induce dipoles, charges, dispersion contributions and hydrophobicity.
You can get a copy of the manual in order to familiarize yourself with this new version.
- Current version: 9.11
- Theoretical Background and Practical Examples, Version 9.11 (2011): PDF) - Official Version 9.11, 2012
- Molaris Reference Manual, Version 9.11 (2011): (PDF) - Official Version 9.09, 2009
- In order to obtain the program, send us an e-mail (ztchu@usc.edu or alternatively warshel@usc.edu) and we will provide you with the latest version.
- Tutorial of the EVB parameters refinement using Mathematica software Refining_EVB_parameters.nb
- References:
- Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the POLARIS and ENZYMIX Programs, F. S. Lee, Z. T. Chu, and A. Warshel, J. Comp. Chem. 14,161 (1993).
- Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease, Y.Y. Sham, Z.T. Chu, H. Tao and A. Warshel, PROTEINS: Structure, Function, Genetics, 2000, 39, 393-407.
Program ChemSol is designed for the calculations of solvation energies
by using Langevin Dipoles (LD) model of the solvent and ab initio calculations. The program can be also used on-line.
- Current version: 2.1
- Reference Manual in PS format
In case of difficulty downloding the Reference Manual from above, you can download the Manual from here Reference Manual (in PDF Format)
- In order to obtain the program, go to the public FTP server at ftp://ftp.usc.edu/pub/warshel/cs2
You may also download the progam from here ChemSol (in TAR Format)
- References:
- Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parameterization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution, J. Florián and A. Warshel, J. Phys. Chem. 101, 5583-5595 (1997).
- Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Lnagevin Dipoles Solvation Model, J. Florián and A. Warshel, J. Phys. Chem. B, 103, 10282-10288 (1999) .
This program has been used extensively in studies of spectroscopic
and conformational properties of molecules in solution and proteins. Some
of it's features include Quantum Mechanical calculations of solvated conjugated
molecules, normal modes analysis, electronic spectra (UV and CD) studies,
Resonance Raman of biological cofactors in protein, charge transfer states
in solution and in molecular crystals, photochemical and redox properties,
and conducting polymers.
- Current version:
- In order to obtain the program, first send us an e-mail (ztchu@usc.edu or, alternatively, warshel@usc.edu) and we will provide you with a temporary version
- References:
- Quantum Mechanical Consistent Force Field (QCFF/PI) Method: Calculations of Energies, Conformations and Vibronic Interactions of Ground and Excited States of Conjugated Molecules, A. Warshel, Israel J. Chem. 11, No.5, 709 (1973).
Last Updated: 15th July, 2011.