Just short comment to this, although I did not read in detail.
Gas phase QM benchmarks are of course very important, but
per se do not necessarily mean the force field fails
in condensed phase simulations. Of course, the closer
to QM becnhmark the better. However, simulations rely
on compensation of errors, which often may greatly
reduce the error transferred to the condensed
phase simulations. Balance of terms is important
and highly empirical.
While simulation people tend to ignore limitations QM
people lacking simulation expertise tend to overemphasize them.
If anyone interested, we have in JPCA somewhere on web in
press paper by Zgarbova et al on Base-Phoshpate H-bonding
in RNAs (essential conserved and difficult interaction
in folded RNAs). While the gas phase errors with respect
to CCSD(T) benchmarks are large, simulations so far
are rather reasonable.
Best wishes, Jiri
On Fri, 23 Sep 2011, Qiantao Wang wrote:
> Date: Fri, 23 Sep 2011 10:41:08 -0400
> From: Qiantao Wang <qiantao.wang.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] XH/pi (X=C, O,
> N) interactions and stacking interactions in AMBER
>
> Hi Rajesh,
>
> FYI, this paper may anwser you 2nd question to some extend.
>
> C.D. Sherrill, B.G. Sumpter, M.O. Sinnokrot, M.S. Marshall, E.G.
> Hohenstein, R.C. Walker, I.R. Gould, Assessment of Standard Force
> Field Models Against High-Quality Ab Initio Potential Curves for
> Prototypes of π- π, CH/π, and SH/π Interactions, J. Comput. Chem. 30
> (2009) 2187-2193.
>
> Regards,
>
> Qiantao Wang
>
> On Thu, Sep 22, 2011 at 7:24 PM, Rajesh Raju
> <rajesh.raju.mail.chem.tamu.edu> wrote:
>> Dear AMBER users,
>>
>> I am just curios about to know how AMBER treats CH/pi, OH/pi NH/pi
>> type of interactions and stacking interactions. Does the van der wall
>> interatcion terms are sufficient enough to model stacking ch/pi and
>> stacking interactions as the major compent of this interactions are
>> dispersion forces..
>>
>> Any explanations or suggestion appreciate
>>
>>
>> Rajesh
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 23 2011 - 09:00:02 PDT
