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Finally, after a huge and vast search i found Chem Bio Office software version 12, with its serial and activation codes. Chem Bio Office(v12) contains ChemDraw 12.0, Chem 3D Pro, Chem Script, Chem Bio finder applications along with updated license keys, Inventory, Chem BioAssay and Chem Note Book applications and Maestrec for NMR predictions were included in this.

It is a new version which is available free and it contains the following new modifications from thr earlier versions.

What's New? in this Chem Office 12.0?

Chem & Bio Draw has long been the preferred tool for illustrating chemical concepts. Chem & Bio Draw 12.0 introduces a variety of improvements and new features not found in earlier versions. The new features in this latest version of Chem & Bio Draw are briefly described below. You can find more information on these and other features throughout the manual and online Help.

Disulfide Bridges

When you create a disulfide bond between cysteine residues, Chem & Bio Draw 12.0 will create the disulfide bridge for you. For information, see "Disulfide Bridges".

Bonding from Sequence Atoms

In Chem & Bio Draw 12.0, you can create bonds from specific atoms in DNA, RNA, and protein sequences. The bonds are retained even if you expand or collapse the sequence labels. See "Bonding from sequences".

Rotation Centers

Using Chem & Bio Draw 12.0, you can rotate your drawing around an atom, an arbitrary center, or any other location on screen. See "Rotating Objects".

Export to SVG

In Chem & Bio Draw 12.0, you can export your drawings in the Scalable Vector Graphics (SVG) format. SVG is an XML-based format often used to describe two-dimensional vector graphics. To save a drawing as an SVG file, go to File & go to Save As.

Structure & Name Improvements

Ring structure recognition has been greatly improved in the Structure & go to Name feature for Chem & Bio 12.0. You can now apply Structure & go to Name to more complex ring assemblies, fused ring systems, and bridged fused ring systems than was possible with earlier versions of Chem & Bio Draw:

Structure & Name supports ring assemblies that consist of two or more rings or ring systems.

Structure & Name in earlier versions of the Chem & Bio Draw supported fused ring systems that consisted of only 2-3 rings. In Chem & Bio Draw 12.0, Structure & Name has been enhanced to recognize much more complex systems.

Structure & Name supports bridged fused ring systems in Chem & Bio Draw 12.0.

For information on Structure & Name, see "Struct=Name ".

Read more...

What is Molecular Modelling?

Molecular modeling 

encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, drug design, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling techniques is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (the Molecular mechanics approach), or explicitly modeling electrons of each atom (the quantum chemistry approach).

List of Free Softwares available

This is a list of computer programs that are predominantly used for molecular mechanics calculations.


Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, REM - Replica exchange method, QM - Quantum mechanics, Imp - Implicit water, HA - Hardware accelerated.

Y - Yes.

I - Has interface.

Name	View 3D	Model Builder	Min	MD	MC	REM	QM	Imp	HA	Comments	License	Website
Abalone	Y	Y	Y	Y	Y	Y	I	Y	Y	Biomolecular simulations, protein folding.	Free	Agile Molecule
ACEMD[1]			Y	Y					Y	Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA.	Basic version free. Commercial version available.	Acellera Ltd
ADUN[2]			Y	Y			Y	Y		Charmm, AMBER, user specified (through force field markup language, FFML), QM/MM calculations with Empirical Valence Bond (EVB); Framework based (GNUStep/cocoa); SCAAS for spherical boundary conditions	Free	adun.imim.es
AMBER[3]		Y	Y	Y		Y		Y			Not free	ambermd.org
Ascalaph Designer	Y	Y	Y	Y	Y	Y	I	Y	Y	Molecular building (DNA, proteins, hydrocarbons, nanotubes). Molecular dynamics. GPU acceleration.	Free & Commercial	Ascalaph Project
Automated Topology Builder (ATB)		Y	Y							Automated molecular topology building service for small molecules (< 99 atoms). GROMOS, GROMACS, CNS formats with validation Repository for molecular topologies and pre-equilibrated systems	Free for academic use	Automated Topology Builder
Avogadro	Y	Y	Y				I			Molecule building, editing (Peptides, small molecules, crystals), Conformational analysis, 2D/3D conversion. Extensible interfaces to other tools.	Free, open source	Avogadro
Balloon		Y	Y							2D/3D conversion and conformational analysis.	Free to use, closed source	Åbo Akademi
BOSS			Y		Y		Y			OPLS	Commercial	Yale University
CHARMM		Y	Y	Y	Y	I	I	Y		Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm)	Not free	charmm.org
Chemitorium	Y	Y								Free 2D/3D graphical organic molecule builder, viewer and visualisation tool.	Free	link
ChemSketch	Y	Y	Y							Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified CHARMM for fast stable inaccurate optimization of single molecules up to 1000 atoms	Free	Advanced Chemistry Development, Inc.
COSMOS	Y	Y	Y	Y	Y		I			Hybrid QM/MM COSMOS-NMR force field with fast semi-empirical calculation of electrostatic and/or NMR properties. 3-D graphical molecule builder and viewer.	Free (without GUI) and commercial	COSMOS Software
Culgi	Y	Y	Y	Y	Y					Atomistic simulations and mesoscale methods.	Not free	Culgi BV
Desmond	Y	Y	Y	Y		Y				High Performance MD. Comes with a comprehensive GUI for building, visualizing, and reviewing results as well as calculation setup up and launching.	Free and commercial	D. E. Shaw Research
Discovery Studio	Y	Y	Y	Y	Y		Y	Y		Discovery Studio is a comprehensive life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Capabilities include, small molecule simulations, QM/MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc.	Closed source/Trial available	Accelrys
fold.it	Y / I	Y	Y	Y	Y	Y	I			University of Washington and The Baker Labs. Structure prediction. Protein folding.	Free, download	fold.it download page
FoldX	I	Y	Y							Energy calculations and protein design	Free for academic use	CRG
GoVASP	Y		I	I			I			GoVASP is a sophisticated graphical user interface for the Vienna Ab-Initio Simulation Package (VASP). GoVASP comprises tools to prepare, perform and monitor VASP calculations and to evaluate and visualize the computed data.	Closed source/Not free/Trial available	Windiks Consulting
GPIUTMD	I	I	Y	Y		I			Y	GPIUTMD stands for Graphic Processors atIsfahan University of Technology for Many-particle Dynamics. It performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs to attain a level of performance equivalent to hundreds of processors on a fast cluster.	Closed source/Not free/Demo available	GPIUTMD
GROMACS				Y		Y			?	High performance MD	Free	gromacs.org
GROMOS			Y	Y						Geared towards biomolecules	Not free	GROMOS Homepage
GULP			Y	Y						Molecular dynamics and Lattice optimization	Free for academic use	https://projects.ivec.org/gulp/
HOOMD-blue			Y	Y					Y	General-purpose Molecular Dynamics highly optimized for GPUs. Includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimization, etc...	Free, open source	http://codeblue.umich.edu/hoomd-blue/index.html
ICM	Y	Y	Y		Y			Y		Powerful global optimizer in an arbitrary subset of internal variables, NOEs, Protein docking, Ligand docking, Peptide docking, EM, Density placement	Not free	Molsoft
LAMMPS			Y	Y	Y		I		Y	Has potentials for soft and solid-state materials and coarse-grain systems	Free	Sandia
MacroModel	Y	Y	Y	Y	Y		I	Y		OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimization, MD. Includes the Maestro GUI which provides visualization, molecule building, calculation setup, job launching and monitoring, project-level organization of results and access to a suite of other modelling programs.	Not free	Schrödinger, LLC
MAPS	Y	Y	Y	Y	Y		Y		Y	Building, visualization and analysis tools in a single user interface together with access to multiple simulation engines.	Closed source/Trial available	Scienomics
Materials Studio	Y	Y	Y	Y	Y		Y	Y	Y	Materials Studio is a software environment that brings the materials simulation technology to desktop computing, solving key problems throughout the R&D process.	Closed source/Trial available	Accelrys
MedeA	Y	Y	Y	Y	Y		Y			MedeA combines leading experimental databases and major computational programs like the Vienna Ab-Initio Simulation Package (VASP), LAMMPS, GIBBS with sophisticated materials property prediction, analysis, and visualization.	Closed source/Trial available	Materials Design
MCCCS Towhee					Y					Originally designed for the prediction of fluid phase equilibria	Free	Towhee Project
MDynaMix				Y						Parallel MD	Free	Stockholm University
MOE	Y	Y	Y	Y			I	Y		Molecular Operating Environment	Commercial	Chemical Computing Group
MOIL	Y	Y	Y	Y						Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling.	Free	link
molecools	Y	Y								Simple Javascript molecular visualization tool		link
MOLDY				Y						Parallel, only pair-potentials, Cell lists, modifiedBeeman's algorithm	Free	Moldy
ORAC			Y	Y		Y				A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level	Free, open source	ORAC download page
NAB[4]		Y								Generation of Models for "Unusual" DNA and RNA	Free	Case group
Packmol		Y								Builds complex initial configurations for Molecular Dynamics		link
Prime	Y	Y	Y		Y		I	Y		Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized		link
Protein Local Optimization Program		Y	Y	Y	Y					Helix, loop, and side chain optimization. Fast energy minimization.	Not free	link
p4vasp	Y	Y								Python-based viewer, structure builder and VASP results browser. Shows band-structure, charge densities and simulates STM images.	Free, open source	p4vasp.at
PyMol	Y	Y								Python-based viewer, many plugins to other software. Some mutagenisis.	Free, open source	PyMol.org
QMOL	Y									Protein viewer, provided byDNASTAR	Free	DNASTAR, Inc.
RasMol	Y									Fast viewer	Free	RasMol
Raster3D	Y									High quality raster images	Free	University of Washington
RedMD[5]	I	Y	Y	Y	Y					Reduced MD. Package for coarse-grained simulations.	Free on GNU Licence	University of Warsaw, ICM
StruMM3D (STR3DI32)	Y	Y	Y	Y	'		'			Sophisticated 3-D molecule builder and viewer, advanced structural analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking and the handling of complexes.	The 200 atom version is free	Exorga, Inc.
Selvita Protein Modeling Platform	Y	Y	Y		Y					Protein structure prediction,homology modeling, ab initiomodeling, loop modeling, protein threading	Commercial	Selvita Ltd
SimBioSys' MoDeST (Molecular Design Software Toolkit)	Y	Y	Y						Y	molecular docking, scoring functions for docking, "ligand-based", "fragment-based", "de-novo"	Not Free	SimBioSys Inc.
Spartan	Y	Y	Y		Y		Y	Y		Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, spectra, reactivity, and selectivity.	Commercial, Trial Available	Wavefunction, Inc.
SwissParam										Web server to determine automatically parameters and topologies for small organic molecules, for use with the CHARMM all atoms force field. Files can be used with CHARMM and GROMACS.	Free for academic. CHARMm licence required for commercial usage.	SwissParam.
TeraChem			Y	Y			Y		Y	High performanceGPU-acceleratedab initio Molecular Dynamics and TD/DFT software package for very large molecular or even nanoscalesystems. The software runs onNVIDIA GPUs and64-bit Linux, and is based on heavily optimizedCUDA code.	Closed source / Trial licenses available	PetaChem LLC
TINKER	I	Y	Y	Y	Y		I	Y		Software tools for molecular design	Free	Washington University
Tremolo-X	I		Y	Y						Fast, parallel MD	Not Free	Tremolo-X
UCSF Chimera	Y	Y	Y							Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development.		University of California
VEGA ZZ	Y	Y	Y	I	Y			Y	Y	3D viewer, multiple file format support, 2D and 3D editor, surface calculation, conformational analysis, MOPACand NAMDinterfaces, MD trajectory analysis, molecular docking, virtual screening, database engine, parallel design,OpenCLacceleration, etc.	Free for academic use	VEGA ZZ Web site
VLifeMDS	Y	Y	Y		Y		I		Y	Complete Molecular Modelling Software, QSAR, Combinetorial Library generation, Pharmacophore, Cheminformatics, docking, etc.	Not free	Vlife Sciences Technologies
VMD +NAMD	Y	Y	Y	Y		Y		Y	Y	Fast, parallel MD, CUDA	Open source, free to academics	Beckman Institute
WHAT IF	Y	Y	I	I	I					Visualizer for MD. Interface to GROMACS.	Not free	WHAT IF
xeo	Y	Y								open project management for nanostructures		link
YASARA	Y	Y	Y	Y			Y			Molecular-graphics, -modeling and -simulation program	Not free	YASARA.org
Zodiac	Y	Y	Y							Drug design suite		link

If you are a beginner in Molecular Modelling then here a book is for You to download free (OPEN access).

Molecular Modelling for Beginners, Second Edition

Publisher:JohnWiley & Sons Ltd 2008 | 411 Pages | ISBN: 9780470513132 | PDF | 12 MB   

Download Link-1

Download link-2

See the abstracts presented on Molecular modelling and docking studies in Chemistry in a Workshop held on Molecular modelling-2012---See here

In Next post, I try to evaluate all the softwares of Molecular modelling one by one and until then......Enjoy :)