Chemical Informatics Letters

Volume 13, Issue 6; December 2006

Editor: Jonathan M Goodman

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Survey of molecular modelling programs

Last reviewed in Chemical Informatics Letters 2005, 11, #6, 61. This list excludes the major commercial molecular modelling packages and concentrates on programs for which the source code is available in some form and which are available freely or cheaply. Usually there is a license agreement restricting what may be done with the source code. Also of interest is WebMO: a World Wide Web-based interface to computational chemistry packages (current version is 6.1)

AMBER: Originally developed by Peter Kollman, and now maintained by Professor David Case' group at the Scripps Research Institute and collaborators, AMBER costs $400 for an academic license, which includes source code. All purchases of Amber version 9 was released on March 29th, 2006.
AMMP: A molecular mechanics and dynamics program written in C by Professor Robert Harrison at Georgia State's Computer Science Department. The program appears to have been last updated in 2002, and the current Windows release version is 1.6.
B: B, formerly Biomer; Free; Source Code; Java. Has moved from its old location to Professor David Case' group at the Scripps Research Institute. The page was last updated on 11th October 2002.
CHARMM: The CHARMM Development Project is a network of developers working with Professor Martin Karplus. CHARMM is available for a $600 licensing fee. Latest release: CHARMM c32b2, February 2006.
COLUMBUS: COLUMBUS provides high-level multi-reference ab initio molecular electronic structure calculations, developed by Hans Lischka at the University of Vienna, amongst others. The latest version is 5.9.1.
CPMD: A plane wave/pseudopotential implementation of Density Functional Theory. The CPMD group is coordinated by Professor Michele Parrinello (ETH Zurich) and Dr Wanda Andreoni (Manager of the Computational Material Science Group at IBM Zurich Research Laboratory). An e-mail discussion list is available to discuss the program, which is active in December 2006. Last updated May 2004. Current version is v3.11.
DALTON: A quantum chemistry program using SCF, MP2, MCSCF or CC wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces. The main authors are T. Helgaker, H. J. A. Jensen, P. Jorgensen, J. Olsen, K. Ruud, H. Ågren. Dalton 2.0 was released on March 4 2005.
DeMon: A DFT code from the University of Montreal. Version 2.3 was released in November 2006.
Dirac: Relativistic ab initio molecular calculations developed at the University of Southern Denmark by Hans Jorgen Aagaard Jensen and others. Latest version is Dirac04, released in 2004.
FSatom: Free software project for atom scale simulation, which will incorporate Molecular Dynamics and Force Fields, Quantum Chemistry and Density Functional Methods. The last update appears to be the implementation of the database in mySQL in 2004; the mailing list has one message since February 2004.
GAMESS-UK: Ab initio calculations. A software company, Computing for Science, now administers GAMESS-UK, which remains free to UK academics. Martyn Guest, of the CCLRC, is the main author. Version 7 is now available.
GAMESS-US: Ab initio calculations. The program is maintained by Dr Mark Gordon's research group at the Ames Laboratory. Last updated September 2006.
Ghemical: A computational chemistry software package released under the GNU GPL; C++; Linux. Developed in Finland by Tommi Hassinen and collaborators. Latest version is v2.10, released in August 2006 .
GROMACS: A molecular dynamics package, available under GPL, initially developed by Herman Berendsen at Groningen University. Last modified April 2006 (version 3.3.1).
GULP: A molecular modelling program for periodic solids, gas phase cluseters and isolated defects, written by Julian Gale. Version 3.0.1 is the latest version, which was updated in May 2006.
JoeLib: A Java based cheminformatics (computational chemistry) library, last updated in July 2006 and released under GPL. A Wiki is now available to discuss JoeLib.
LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator, a molecular dynamics code from the Sandia National Laboratory. The current version was released in October 2006.
Minnesota University Solvation Models and Software: Software for solvation models from the groups of Christopher J. Cramer and Donald Truhlar.
MMTK: Open Source Project; Mainly written in Python,with a small amount of C; Konrad Hinsen, from CNRS Orleans, who is also involved with FSatom (vide supra). There is now a MMTK Wiki, which has been updated in November 2006, and a mailing list which was active in September 2006. The current release of MMTK is v2.4.4, and it was updated in 2005. nMOLDYN is an analysis program for molecular dynamics simulations, which interacts with MMTK. There is a nMOLDYN Wiki. The current version is v2.2.2 and it was updated in 2005.
MOIL: MOIL is public-domain molecular modeling software, written in the group of Ron Elber. Current version is MOIL 9.1, released in June 2004.
MOLPRO: A complete system of ab initio programs for molecular electronic structure calculations developed by Professor Peter Knowles at Cardiff University and Professor Hans-Joachim Werner at Stuttgart University. Version 2006.1 was released in June 2006.
MPQC: MPQC is the Massively Parallel Quantum Chemistry Program, released released under GPL. The lead developer is Curtis Janssen of Sandia National Laboratories. The latest release is v2.3.1 (March 2006).
NWChem: A computational chemistry package that is designed both for workstations and high-performance parallel supercomputers, developed in the William R Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory, USA. Version 5.0 is the latest version, and the documentation was updated in September 2006.
PSI3: The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules, developed by researchers from Viginia Tech, Georgia Tech, the Oak Ridge National Laboratory and Bethel University. The latest version psi-3.2.3, released in October 2005.
Tinker: A free, full source code (Fortran) molecular mechanics and dynamics program, written in the Ponder Lab. Version 4.2 became available in June 2004.
Vigyaan: Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry, which includes a number of chemistry programs ( Ghemical; Jmol; MPQ; PSI3; XdrawChem) The latest stable version is v 1.0 which was released in 2005.
YUP: Yammp under Python. There are several methods for energy minimisation, molecular dynamics and Monte Carlo. From the Harvey Lab at the Georgia Institute of Technology. Version 1.0.061201 was released on December 15, 2006.

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New CAS names

CAS has decided to make changes to the way it names molecules. These affect large groups of molecules, including ylides, (abolished to make way for inner salts), preferred tautomeric forms, the order of precedence of amino acids, and almost three thousand stereoparents (compounds whose names imply particular stereochemistries).

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Molecular Descriptors

The Milano Chemometrics and QSAR Research Group, led by Roberto Todeschini, has released a new website devoted to molecular descriptors.

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Are patents good for pharmaceuticals?

The ACS (The American Constitution Society, rather than the American Chemical Society) notes that a General Accounting Office report (PDF) concludes current patent law discourages drug companies from developing new drugs. Joseph Stiglitz points out the problems the system causes for developing countries.

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Google patent search

Google can now search patents in the US patent office.

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How big is PubChem?

PubChem now has over fifteen million entries. In March 2006, Reactive Reports gave a figure of only eight and a half million compounds of which five and a half million were unique.

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SORD

The Selected Organic Reactions Database is capturing chemistry recorded in theses and dissertations but never published. Co-founded by Dick Wife, it has been the subject of a JISC consultation and uses ACD technology.

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Mendeleev and other peoples tables

How important was Mendeleev? A new book shows how others were also involved in the development of periodic tables. Mendeleev's fame is assured in Russia, however, for his development of vodka technology.

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MyStructure

MyStructure is an open-source plug-in for MySQL that stores chemical structures and calculates descriptors and properties.

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XML

Has the XML decade just finished? IBM has just published an issue of its systems journal, called Celebrating 10 Years of XML.

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CDK

The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics. It originated in Christoph Steinbeck's group at Cologne University Bioinformatics Center.

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Linux4chemistry

Linux4Chemistry, a list of chemistry resources for Linux, is now hosted at Dublin City University, and maintained by Noel O'Boyle.