Re: [AMBER] non-bonding parameters

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 19 Nov 2010 10:02:21 -0500

Hi Eliac,

LEaP converts them for you. The two parameters are simply sigma and
epsilon, in the respective amber units (, kcal/mol, etc.). When it
converts them, it actually converts pairs, according to the formulas on the
refs I sent in the last email. If you want examples for how they should
appear in an frcmod file, see any of the frcmod/parm files in
$AMBERHOME/dat/leap/parm .

Hope this helps,
Jason

On Fri, Nov 19, 2010 at 8:59 AM, Eliac Brown <eliacbrown.yahoo.com> wrote:

> 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
> >
>
>
>
>
> _______________________________________________
> 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
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Received on Fri Nov 19 2010 - 07:30:03 PST
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