Thesis (Ph.D.) - Cairo University - Faculty of Science - Department of Biophysics

A key concept in the development of the generalized force fields is to assign types to atoms taking the chemical environments into account. But unfortunately, the concept of atom typing restricts the chemical environments to a very narrow band in the infinitely large organic space. Actually, newly developed molecules and hetero-compounds have a weak chance to make use of these force fields. On the other hand, the researchers suffer working with the automated force field development tools because of their multiple and diverse requirements. In the present work, we have developed OnclickFF program to supply the optimized force fields of the individual molecules with the minimal requirements. This program enables the researchers to parameterize the harmonic and torsional parameters of their own molecules by a double click on a portable script. The current version of this program requires the formatted check point and the potential energy surface files supplied by Gaussian 09, in addition to the topology and the parameter files in CHARMM format. An optional input file, the configuration file, is required if the researchers want to introduce their own constraints on the parameterization steps. OnclickFF program detects the full sets of the internal coordinates, checks them for stability and gives the appropriate suggestions and warnings

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