On 2/27/15 2:00 AM, soumadwip ghosh wrote:
Dear users,
I have a query about some reviews one a paper which I
submitted recently. It deals with the binding of molecular ions with double
stranded DNA segments. My questions are-
1. Is it customary to take into account The centre-of -mass for DNA grooves
or backbones while calculating RDF? Without that being taken into account,
what kind of artifacts are to be seen?
Dealing with RDFs or occupancies around DNA is extremely challenging. Normal
RDF lack sensitivity and do not fully describe the behavior of ions around DNA,
especially given the asymmetry between major and minor grooves. See, for
instance, dx.doi.org/10.1021/ja0629460
2. Why is it necessary to show the running co-ordination number up to the
first solvation shell? I have calculated the excess cordination number for
each ions in DNA up to half of the box length using the Kirkwood-Buff
integrals. But I think there is a confusion between running coordination
and the excess coordination number. They state that if a coordination number
3. They have asked about the CHARMM 27 force field being outdated now..How
is this true?
Yes. There are specific improvements in CHARMM36 for DNA and RNA, with a
reparametrization of some important backbone torsions in DNA that have
implications for sampling substates of B-DNA and correct sugar puckering.
-Justin
Please help me out in addressing the reviews. Thanks for your help in
advance.
P.S: I did not take the center-of-mass of molecular ions into account. I
dont think it is wrong for a small molecule..
Regards
Soumadwip Ghosh
Research Fellow
IITB, Mumbai
India
--
==
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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