Dear Jit,
I would tell the strategy is OK, at the tactical level
you will have to make specific decisions based on specific
situation in your project/system, including consideration
of potential bias introduced by the simulation, which might
require to investigate also the PES in proximity of the MD
points.
It may happen that some referees might complain that this
is "heterogenou approach and QM should not be applied on
MM geometries". Probably trying to downgrade applicability
of the QM technique applicability.
This is not justified, since good force field
should be mimicking the superior QM data and thus
applying QM based on MM geometries is possible. The above
negative statement would be justified only in
case when the force field is really so bad
that the geometries are totally irrelevant.
We have more and more data showing that using QM after MD
to refine energetics may be very useful.
best wishes, Jiri
P.S.
I give below some papers where we used either directly X-ray or
MD to take geometries.
D. Vlieghe, J. Sponer, L. Van Meervelt. Crystal structure of d(GGCCTTAAGG)
complexed with DAPI reveals novel binding mode. Biochemistry 38, 1999,
16443-16451
J. Sponer, A. Mokdad, J. E. poner, N. pakov, J. Leszczynski, N. B.
Leontis:Unique tertiary and neighbor interactions determine conservation
patterns of cis Watson-Crick A/G base pairs. Journal of Molecular Biology
330, 2003, 967-978
K. Reblova , J.E. Sponer, N. pakov, I. Beeov, J. Sponer: A-Minor Tertiary
Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical
Analysis. Journal of Physical Chemistry B, 2011, 115, 2011, 13897-13910
D. Svozil, P. Hobza, J. poner: Comparison of intrinsic stacking energies
of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we
determine correct order of stability by quantum-chemical calculations?
Journal of Physical Chemistry B 114, 2010, 1191-1203
On Wed, 18 Jul 2012, jit mukherjee wrote:
> Date: Wed, 18 Jul 2012 10:02:34 +0530
> From: jit mukherjee <jitiitkgp.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with
> amber
>
> Dear Jiri Sponer and all Amber users,
> In the previous reply, Jiri Sponer said, "...Constraining the geometries
> close to exp (or explicit solvent MD) should work".
> So, After doing an explicit solvent MD(real experimental situation),if I
> take the simulated structure as the standard one and calculate single point
> anergy and properties with a high level dft-disp method, will it be
> reasonably accurate? Please give your view.
>
> Regards,
> jit mukherjee
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 18 2012 - 03:00:02 PDT
