Chemical Informatics Letters

Volume 11, Issue 6; December 2005

Editor: Jonathan M Goodman

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Survey of molecular modelling programs

Last reviewed in Chemical Informatics Letters 2004, 7, #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

AMBER: Originally developed by Peter Kollman, and now maintained by Professor David Case' group at the Scripps Research Institute and collaborators, AMBER 8 costs $400 for an academic license, which includes source code. _ All purchases of Amber 8 after December 1, 2005 will be eligible for a free upgrade to Amber 9, when it is released.
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.
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 33, August 2005.
CPMD: A plane wave/pseudopotential implementation of Density Functional Theory. The CPMD group is coordinated by Professor Michele Parrinello (Director of the Swiss Center of Scientific Computations and Professor at the ETH Zuerich) 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. Last updated May 2004. Current version is v3.9.2.
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.
FSatom: Free software project for atom scale simulation, which will incorporate Molecular Dynamics and Force Fields, Quantum Chemistry and Density Functional Methods. It is not clear if this program has been updated since 2003; the mailing list has not been active 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 June 2005.
Ghemical: A computational chemistry software package released under the GNU GPL; C++; Linux. Developed in Finland by Tommi Hassinen and collaborators. Latest version is v1.02, released in July 2005.
GROMACS: A molecular dynamics package, available under GPL, initially developed by Herman Berendsen at Groningen University. Last modified October 2005 (version 3.3).
GULP: A molecular modelling program for periodic solids, gas phase cluseters and isolated defects, written by Julian Gale. Last updated June 2004.
JoeLib: A Java based cheminformatics (computational chemistry) library, last updated in January 2005 and released under GPL.
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 this month. The current release of MMTK is v2.4.4, and it was updated in 2005.
nMOLDYN: 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.
MOLPRO: A quantum chemistry package developed by Professor Peter Knowles at Cardiff University and Professor Hans-Joachim Werner at Stuttgart University.
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 v2.3.0 (October 2005).
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 4.7 became available in March 2005.
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)
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 1.0.060101 was released on December 21, 2005.

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Guides to patent searching

Two guides to patent searching are available from Queen's University, Ontario, both as PDF files: U.S. Patent Number Guide and U.S. Patent Classification - Classes by Title.

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Tim Berners-Lee blog

A new blog from the founder of the WWW.

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Chemical words

Have you ever wondered how many words can be spelled using chemical symbols? This page has the answer.

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Geochemical Transactions

Geochemical Transactions is an open-access journal, published by BioMed Central from January 2006. It was an RSC journal, moved to the American Institute of Physics in 2004. Under the new system, authors pay £800 for article processing charges, although UK academics receive an automatic waiver of this fee.

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Wikipedia Semi-protection Policy

How can the Wikipedia protect itself from malicious and inaccurate updating? The policy has just changed to semi-protection, which prevents unregistered editors and editors with accounts newer than four days from editing pages which have been selected to require special protection. This approach might be regarded as hemi-demi-semi-protection, at most, but it may well be sufficient to improve the quality of Wikipedia, and is supported by Jimbo Wales the founder of Wikipedia. Fundraising to support the Wikipedia is on-going.

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QSAR Descriptor Dictionary

QSAR uses a huge number of descriptors: here is a dictionary.

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Various Conferences

The First European Workshop in Drug Synthesis will be held in Siena, May, 14 - 19, 2006. The Infonortics International Conference for Science and Business Information meeting will be held in Nîmes, France 22-25 October 2006. The 2nd International Symposium on Computational Life Science will be held at Cambridge University, 27 - 29 September 2006.

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Top 500 computers

An updated list of the world's 500 most powerful computers has its first UK entry at 33 (weather forecasting), and HPCx, the UK national supercomputer service, and 46. The top chemistry-site is at RIKEN, number 39.

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Thermochemical Properties

This site contains Java applets which estimate thermochemical properties, including boiling point, viscosity and solubility parameters. This is a part of the Virtual Material and Process Simulation Center which also calculates molecular orbitals and other properties.

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Are patents a good thing?

Should owners of patents worry about the value of their intellectual property? Would a reduction in patent use be a bad thing? Perhaps everything is working well.

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Bad science

Bad science is a column which lists examples of bad science, run by Dr Ben Goldacre. No bad science, despite its opposite title, is similar, except that it is tightly focussed on the fields of thermal analysis and rheology.