Hi Jason,
I run sqm with the option "printdipole=1"
the dipole moment that SQM output is for the AM1 before the bond charge correction ..AM1-BCC is
final partial charges in prepi file
in sqm.out for example the AM1 charge on nitrogen in cyano group of biphenylcyano molecule is
so different from AM1-BCC
sqm.out 14 N -0.038
ANTECHAMBER_AM1BCC_PRE.AC
ATOM 14 N 2 -8.532 1.150 0.912 -0.038000 n1
ANTECHAMBER_AM1BCC.AC
ATOM 14 N 2 -8.532 1.150 0.912 -0.363800 25
this mean i have to work out the dipole moment using the partial charges in prepi file
i just need to clarify this matter
thanks
Fatima
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Wednesday, November 05, 2014 3:21 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AM1-BCC dipole moment
On Wed, Nov 5, 2014 at 10:10 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Wed, Nov 05, 2014, CHAMI F. wrote:
>
> > when using antechamber to derive AM1-BCC partial charges ..where to look
> > at for the dipole moment
>
> I'm pretty sure that you have to compute this yourself, using the output
> charges and positions. Note: although the charges are fixed, the dipole
> moment depends upon what conformation you choose to analyze, so there is no
> single number for the dipole moment.
>
FWIW, there is a "printdipole" input option for sqm, so you can print the
QM dipole moment for a specific conformation.
I don't think antechamber ever sets this variable, so you would need to run
sqm by hand (you can always modify the sqm input file that antechamber
generates by adding "printdipole=1" to it) in order to get that information.
If, on the other hand, you want the MM dipole moment, you would likely need
to compute that by hand.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 10 2014 - 06:00:04 PST
