[gmx-users] Pi stacking

Debayan Chakraborty debayan.ch at gmail.com
Wed Apr 15 09:46:25 CEST 2015

As far as I know, AMBER force-fields tend to overestimate the stacking
interactions in nucleic acids, whereas CHARMM tends to understabilize them.
The Chen and Garcia paper talks extensively about it (HIgh-resolution
reversible folding of hyperstable RNA tetraloops using molecular dynamics
simulations (PNAS 2013)) talks extensively about it. In fact, the authors
tried to correct the overstacking problem by reparametrising the VDW
parameters with respect to benchmark CCSD(T) calculations on nucleic acid
dimers (see the supp info). WIthout these corrections, there was lot of
kinetic trapping involved when folding was attempted from the denatured
state using REMD. This paper would be a good  place to start, and check out
the cross references as well.

Debayan Chakraborty,
PhD Student,
Chemical Physics,
Department of Chemistry,
University of Cambridge

On Wed, Apr 15, 2015 at 7:03 AM, soumadwip ghosh <soumadwipghosh at gmail.com>

> Hi all,
>         I want to ask a very general question which was asked by one of the
> reviewer of my paper. I have shown the stacking between different base
> pairs of a single stranded DNA at different salt concentration. The
> corresponding distances between the stacked base pairs were estimated using
> g_dist and the energy terms were calculated using the g_energy and
> selecting the coul:SR and LJ:SR parameters together between two stacked
> residues which were specified as energy groups in the md.mdp file prior to
> the final mdrun. What he has asked me is 'what the pi-stacking interactions
> actually correspond to (in the real world) and how well these are captured
> in the empirical force field description.' I know the pi-stacking in
> principle is a sum of non-bonded electrostatic, dispersive , induced and
> exchange term, basically a sum of non-bonded Coulomb and VDW terms within a
> specified cut-off. How well these terms are captured in the force field
> (CHARMM 27 which I used) is something I dont know. Do I have to cite some
> references to show that others have calculated pi-stacking in a similar
> manner or something more relevant to the CHARMM27 force field?
> I am stuck with this query..Any kind of help would be greatly appreciated.
> Thanks and regards,
> Soumadwip Ghosh
> Research Fellow,
> IIT, Mumbai
> India
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