Arden Perkins wrote:
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.
Please do not double-post. I answered your first (identical) post already:
http://lists.gromacs.org/pipermail/gmx-users/2010-March/049578.html
-Justin
Arden Perkins
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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