Dear Hovakim Actually it is possible that the ethidium bromide is indeed intercalating in the DNA, because this is expected to happen (experimentally) but if you really see the intercalation, it could be just luck. The time scale needed, in order that such even happens in classical molecular dynamics simulations, is usually very large. Nevertheless, the presence of intercalation could be easily checked by visual inspection of the structures and by looking at the values of some key base-pair step parameters, such as rise and twist. In my opinion, it is better to generate an artificial gap in the DNA structure, in order to sample the intercalation binding mode as a reasonable starting point for MD simulations.
Best regards Paulo Netz On Thu, Sep 27, 2012 at 3:15 AM, Hovakim Grabski <[email protected]>wrote: > Dear Gromacs users, > > I've been running several simulations involving 26 base pairs B-DNA and > ethidium bromide. > I used Autodock vina for finding inital binding sites and found one in the > small groove. > After that I ran a simulation of 14 ns. > When I check the rmsd of Ethidium Bromide,there's a sudden change. > Is there any chance I could see intercalation? > P.S. Or I should create an artifical gap between dna bases and then set > up a simulation? > Thanks in advance, > Best regards, > Hovakim Grabski > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
