Re: [AMBER] non-bonding parameters

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 19 Nov 2010 09:49:15 -0800

Leap only understands R*, so my belief is that sigma needs to be
manually converted to R* for leap.

Bill


> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber




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Received on Fri Nov 19 2010 - 10:00:04 PST
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