[gmx-users] Pi stacking

Justin Lemkul jalemkul at vt.edu
Wed Apr 15 14:31:36 CEST 2015

On 4/15/15 3:46 AM, Debayan Chakraborty wrote:
> As far as I know, AMBER force-fields tend to overestimate the stacking
> interactions in nucleic acids, whereas CHARMM tends to understabilize them.

Over all of the ideal stacked base conformations, this is generally true, but 
the magnitude of the error is rather small.  Sequence dependence is important 
for the interpretation of the actual system at hand.  Relative to high-level QM 
that we've done, most of the stacking energies (in CHARMM36, but CHARMM27 should 
be very similar) are very good.


> 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.
> Best,
> 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>
> wrote:
>> 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
>> --
>> Gromacs Users mailing list
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.


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


More information about the gromacs.org_gmx-users mailing list