[gmx-users] pi-stacking energy between carbon nanotube and nucleic acids

[Justin Lemkul]

On 4/2/15 7:05 AM, soumadwip ghosh wrote:
> Dear users,
>                    I was wondering which is the more realistic way to find
> out the stacking energy between a DNA base and a single wall carbon
> nanotube. I am interested in evaluating pi-stacking interactions between
> individual residues and a Chiral carbon nanotube. In some of the papers
> they calculate the interaction between DNA strand and carbon nanotube using
> various free energy estimations (MM-PBSA, TBI or free energy perturbation
> techniques) but isn't it the short range LJ forces from
> the appropriate energy groups in the .edr file that should be more
> realistic?
>

The general consensus is that van der Waals interactions dominate (but it is 
geometry-specific), but there are non-negligible electrostatic/polarization 
contributions.  The driving forces behind pi stacking have been addressed very 
thoroughly in work by Sherrill and others using high-level QM.

> Also, when I am calculating RMSD with respect to the initial structure it
> was my expectation that the residue which gets stacked more strongly would
> have the highest magnitude of RMSD as compared to the initial structure but
> I am getting the order reversed. Is there something wrong in my assumptions?
>

Highest RMSD with respect to what state?

-Justin

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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