WEB BASED DOCUMENTATION & TUTORIALS FOR YAMMP

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Adequate on-line documentation is a great asset for any widely used molecular modeling package. Since YAMMP was originally developed only for use at the University of Alabama at Birmingham (UAB), documentation had not previously been regarded as a critical issue. With the establishment of this Research Resource and a series of new collaborations with scientists outside UAB, proper documentation became a high priority. We decided to take advantage of web technology, and we have begun developing complete on-line documentation for YAMMP. From the beginning, we have coupled the documentation to a series of on-line tutorials for educating new users in the principles and practices of using YAMMP for modeling macromolecular systems. The tutorial package has modules aimed at experienced modelers and structural biologists: these focus on the empirical force field used in low resolution YAMMP models. Another set of modules is aimed at the novice modeler: these use simple alkanes to teach the basic principles of molecular mechanics, including force fields and algorithms (energy minimization; molecular dynamics; Monte Carlo; simulated annealing). Since the tutorials assume certain basic mathematical skills, we are also developing tutorials to help students refresh or learn those skills as necessary: these include such concepts as the normal distribution, the Boltzmann distribution, Fourier analysis, and so on.