AmberFFC 1.3 – Convert Force Fields for use with Commercial Molecular Modeling Packages

AmberFFC 1.3

:: DESCRIPTION

AmberFFC creates the AMBER & GLYCAM FF for the Accelrys molecular mechanics modules, FDiscover and CDiscover by transforming the AMBER/GLYCAM topology database and FF parameter files to the Accelrys file format. Thus, the program is useful for any modeler who is interested in (i) using the AMBER & GLYCAM FF with the Accelrys software and (ii) comparing the results obtained with the AMBER and Accelrys modeling packages.

::DEVELOPER

A. Dejoux, P. Cieplak, N. Hannick, G. Moyna, & F.-Y. Dupradeau,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Perl

:: DOWNLOAD

AmberFFC

:: MORE INFORMATION

Citation:

A. Dejoux, P. Cieplak, N. Hannick, G. Moyna, & F.-Y. Dupradeau,
AmberFFC, A Flexible Program to Convert AMBER and GLYCAM Force Fields for use with Commercial Molecular Modeling Packages,
J. Mol. Model., 2001, 7, 422-432,

Open Babel 2.3.2 – Converter for Chemistry & Molecular Modeling Data Files

Open Babel 2.3.2

:: DESCRIPTION

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

::DEVELOPER

Open Babel Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

Open Babel

:: MORE INFORMATION

Citation

Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck, Joerg Kurt Wegner, Egon Willighagen.
The Blue Obelisk – Interoperability in Chemical Informatics.
J. Chem. Inf. Model. 2006, 46, 991-998.

Ghemical 3.0.0 – Molecular Modeling and Editing Package for GNOME

Ghemical 3.0.0

:: DESCRIPTION

Ghemical is a molecular modeling and editing package for GNOME. It integrates a molecular mechanics force field as well as integration with MOPAC and optionally the MPQC package for quantum mechanical calculations. It integrates Open Babel to import/export to a variety of external programs.

::DEVELOPER

Ghemical Team

:: SCREENSHOTS

:: REQUIREMENTS

Linux
GNOME

:: DOWNLOAD

Ghemical

:: MORE INFORMATION

Citation

Tommi Hassinen, Mikael Peräkylä:
New energy terms for reduced protein models implemented in an off-lattice force field.
J Comput Chem 2001 , 22, 1229-1242

MoluCAD 1.034 – Molecular Modeling & Visualization Tool

MoluCAD 1.034

:: DESCRIPTION

MoluCAD is a full-featured molecular modeling and visualization tool designed for Windows. Originally conceived as an aid for students of organic chemistry, MoluCAD has quickly evolved into much more. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Ease of use, premium graphical quality, and computational robustness are the trademarks of MoluCAD.

::DEVELOPER

New River Kinematics

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

MoluCAD

:: MORE INFORMATION

For more information, e-mail: molucad@kinematics.com

MOIL 12.0.3923 – Molecular Modeling Software

MOIL 12.0.3923

:: DESCRIPTION

MOIL is a package for molecular dynamics and modeling. Moil supports the usual set of tools for molecular modeling by classical mechanics, including energy calculations, energy minimization, molecular dynamics, and more.

::DEVELOPER

MOIL team: Thomas Blom, Peter Majek, Serdal Kirmizialtin, and Ron Elber

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
TCL

:: DOWNLOAD

MOIL

:: MORE INFORMATION

Citation

R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker,C. Keasar, J. Zhang and A. Ulitsky
“MOIL: A program for simulations of macromolecules“,
Computer Physics Communications, 91, 159-189(1995)

MaSK 1.3.0 – Molecular Modeling and Simulation Kit

MaSK 1.3.0

:: DESCRIPTION

MaSK (Molecular Modeling and Simulation Kit) is the software that is useful in the visualization of various molecular properties calculated by either GAMESS/Firefly or Gaussian? computational chemistry programs.

::DEVELOPER

Yevgeniy Podolyan

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

:: REQUIREMENTS

Windows

:: DOWNLOAD

MaSK

:: MORE INFORMATION

Citation

Y. Podolyan, J. Leszczynski.
MaSK: A Visualization Tool for Teaching and Research in Computational Chemistry.
Int. J. Quantum Chem. 2009, 109(1), 8-16.

Biodesigner 0.75 – Molecular Modeling & Visualization

Biodesigner 0.75

:: DESCRIPTION

Biodesigner is a molecular modeling and visualization program for personal computers.Biodesigner is capable of creating homologous models of proteins, evaluate, and refine the models.

::DEVELOPER

Piotr Rotkiewicz

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Biodesigner

:: MORE INFORMATION

For further information please contact Piotr Rotkiewicz