OmpF an outer-membrane porin channel of _E. Coli_ posses beta-barrel structure, whose conductivity and gating phenomena are affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature, polyelectrolytes etc. Nucleotides are considered as one of most important metabolite in the cell that have pass through membrane whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable information However, due to the instrument limitation in monitoring ontime submolecular motions occurring during the translocation, theoretical studies attractive, modeling and simulation are inevitable. In this study we calculated the changes in the affinity of OmpF towards pyrimidin at molecular level within channel lumen by Delphi 4, and monitored by VMD 1.8.5. A non-linear Poisson-Boltzmann calculator with definite element integrator found to be appropriate choice to calculate the net energy of OmpF nucleotide interactions at different ion concentration. Our results indicate that upon increasing the ion concentration the OmpF affinity to pyrimidin decreases along the channel axis showing a minimum at the inner mouth of the channel. These observations shed lights to understand the selective molecular translocation means involved in the OmpF
