On 6/11/15 1:40 AM, soumadwip ghosh wrote:
Hello,
I am asked by one of the reviewers of my paper about the
distribution of ions ( Mg2+) bound to a single stranded DNA as a function
of simulation time at different salt concentrations. In order to do that I
have calculated the RDF of ions from the closest atom of DNA using g_rdf
with surf mol and res_com option at different time intervals. The first
peak minima came around 5 angstrom and I calculated the number of ions in
that cut-off at different time intervals with the -cn option of g_rdf. Then
I am plotting it as no.of ions bound to DNA against time. what I want to
ask is there anything wrong with this approach? I have referred to the work
below
http://www.tandfonline.com/doi/pdf/10.1080/07391102.2012.732344
Is there some other ways ( command or tool wise ) where the calculations
are more accurate as far as the ion binding approach is concerned?
Dealing with Mg2+ is complex. The above paper draws similar to conclusions with
what others have seen. Additive models of divalent cations are generally pretty
crude. Mg2+ has a very slow (us - ms) exchange rate with water and about a 12.5
kcal/mol barrier for water dissociation. You're never going to see exchange in
an MD simulation, so if there are direct interactions with the nucleic acid
(which is extremely important for RNA, but I've never heard of that for DNA)
then those won't happen unless you place the ions there specifically or take
them from a crystal structure. The slow dissociation is part artifact, part
reality. Tricky proposition.
As for the issue at hand, I think your method of RDF is very crude. It is
generally of much greater interest to identify the functional groups that
coordinate the ions. You are unlikely to have direct Mg2+ interactions given
the above information, but proximity to actual groups (phosphate, base moieties)
is interesting information that you're completely glossing over.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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