Open Source FreeBSD Chemistry Software

The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data.

RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence of Cbeta chemical shift information: over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. RASP is described here: MacRaild and Norton (2014) RASP: Rapid and robust backbone chemical shift assignments from protein structure. J Biomol NMR doi:10.1007/s10858-014-9813-7

(We have migrated this project to github [June 1 2015)] http://github.com/msg-byu/enumlib). The source files have been removed from sourceforge. Go to github (link above) for the latest copy. <<<< OLD SUMMARY >>>> A Fortran 95 implementation of an algorithm for generating derivative structures of a parent lattice. The algorithm is discussed in detail in: Gus L. W. Hart and Rodney W. Forcade, "Algorithm for generating derivative structures," Phys. Rev. B 77 224115 (26 June 2008) http://msg.byu.edu/papers/GLWHart_enumeration.pdf Gus L. W. Hart and Rodney W. Forcade, "Generating derivative structures from multilattices: Application to hcp alloys," Phys. Rev. B 80 014120 (July 2009) http://msg.byu.edu/papers/multi.pdf Gus L. W. Hart, Lance J. Nelson, and Rodney W. Forcade, "Generating derivative structures at a fixed concentration," Comp. Mat. Sci. 59 101-107 (March 2012) http://msg.byu.edu/papers/enum3.pdf

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

Python software to control Bronkhorst flow controllers via RS232. Works via USB serial converter too.