[gmx-users] Literature for DNA Binding Protein Simulations

[Arden Perkins]

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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