----- Original Message ----- From: Arden Perkins <[email protected]> Date: Wednesday, March 24, 2010 1:35 Subject: [gmx-users] Literature for DNA Binding Protein Simulations To: [email protected]
> > > 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. That sounds ambitious for an undergraduate research project. Observing how a peptide interacts with a DNA strand is a very complex sampling problem even if the peptide and DNA are rigid bodies in implicit solvent. One needs prodigious amounts of sampling even in such cases, let alone explicit solvent ones where they are flexible... Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
