Re: [AMBER] non-bonding parameters

From: Eliac Brown <eliacbrown.yahoo.com>
Date: Fri, 19 Nov 2010 16:09:03 -0800 (PST)

Dear Dr. Jason and Dr. Bill
Thanks for your reply.
But we are not agreed now. The same stuff appears in the papers published on the zinc ion. Some of them converted it and others didn't.
The stote's parameters are: sigma=1.95 and e=0.25
so, what exactly should I use in my frcmod file?
I need to know the correct value before starting my project.
thanks
Eliac
--- On Fri, 11/19/10, Bill Ross <ross.cgl.ucsf.EDU> wrote:

> From: Bill Ross <ross.cgl.ucsf.EDU>
> Subject: Re: [AMBER] non-bonding parameters
> To: amber.ambermd.org
> Date: Friday, November 19, 2010, 5:49 PM
> 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
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> _______________________________________________
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> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > >
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>
> > --
> > 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 - 16:30:03 PST
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