Dear Dr. Jason
Thanks for the reply.
I am fully aware about this two pages, but I still have a problem in using the parameters.
My project on Zinc ion, I want to use stote parameters, according to the paper: sigm=1.95 and e=0.25
so my non-bonding parameters should be:
VDW 1.95 0.25
or convert sigm to r using the formula r=2^(1/6)sigm
I am using amber10
thanks
Eliac
--- On Thu, 11/18/10, Jason Swails <jason.swails.gmail.com> wrote:
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] non-bonding parameters
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Thursday, November 18, 2010, 10:09 PM
> Hello,
>
> See the following:
>
> http://ambermd.org/Questions/vdwequation.pdf
> http://ambermd.org/Questions/vdw.html
>
> Those should clarify.
>
> Good luck!
> Jason
>
> On Thu, Nov 18, 2010 at 2:32 PM, Eliac Brown <eliacbrown.yahoo.com>
> wrote:
>
> > Dear Sir/Madam
> > I am a beginner in using AMBER. I found in amber file
> format, for
> > non-bonding interaction:
> > 'RE' van der Waals radius and the potential well depth
> parameters are read.
> > In other amber related pages, it says atomic radius
> and well depth
> > In a third party, it says amber radius and well depth
> or sigm and well
> > depth
> > what is the correct description for the first term?
> > I know r(min)= 2^(1/6)*sigm
> > thanks
> > E. Brown
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 19 2010 - 06:30:02 PST
