[gmx-users] Literature for DNA Binding Protein Simulations

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 23 16:26:47 CET 2010

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:



> Arden Perkins


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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