I do not think that using PM3 for DNA is the best idea. It is so-so
for the long-range interactions and is so-so for any ion-molecular
interactions (in general)
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Aug 18, 2014 at 9:12 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..
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Received on Mon Aug 18 2014 - 13:00:02 PDT
