Dear GROMACS users, I am interested in running a simulation of a DNA-binding peptide and a short stretch of DNA for an undergraduate research project. The pdb file we will be using is a modified version of the Hickman et. al (2004) Rep structure http://www.pdb.org/pdb/explore/explore.do?structureId=1RZ9 . The file consists of five Rep peptides and one stretch of DNA (approx. 6 helical turns). We will only be simulating one peptide however, at 197 aa. We would like to subject the peptide to different variables in a water-solvated box and then observe its interaction with the segment of DNA to which it binds (such as temperature, ion molarities, etc).
What literature would you recommend I review in order to have a good understanding of the parameters involved in such a simulation? I have run simulations of this peptide in solvated systems before, but I have never attempted one with more than one peptide or a peptide with DNA. Any suggestions would be very appreciated. Arden Perkins
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