PM3 has all of the same terms as any of the other NDDO methods with the
addition of Gaussian screening terms as per the AM1-type methods. Some of
the dispersion corrected methods are implemented in SQM, but you will have
to read carefully about these, as they may not be widely tested or used.
I am pretty sure there are quite a few benchmark papers on various
semiempirical methods, probably including base stacking energies. I would
give the literature a brief survey (Google Scholar is probably sufficient
for this).
Regards,
Brian
On Mon, Aug 18, 2014 at 1:12 PM, Muthukumaran R <kumaran.bicpu.edu.in>
wrote:
> Dear amber users,
>
> I am running QMMM module implemented in the
> Amber 11 package. Here is my input md.in file
>
> imin=0,irest=1,ntx=5,
> nstlim=25000,dt=0.001,
> ntc=2,ntf=2,
> cut=10, ntb=2, ntp=1, taup=1.0,
> ntpr=50, ntwx=50,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> ifqnt=1,
> /
> &qmmm
> qmmask=":18-20,39-41,60-62",
> qmcharge=-5,
> qm_theory="PM3",
> qmcut=10.0,
> qmshake=0,
> writepdb=1,
> /
>
>
> I am using PM3 theory for quantum calculations. Do PM3 method account the
> dispersion effect (electron correlation functions) to model long range
> interactions??
>
> To be more specific while dealing with DNA, PM3 methods includes the
> base-pair stacking interaction energies??
>
> Thanks in advance..
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Mon Aug 18 2014 - 11:30:04 PDT
