Re: [AMBER] non-bonding parameters

From: Eliac Brown <eliacbrown.yahoo.com>
Date: Fri, 19 Nov 2010 16:24:44 -0800 (PST)

Sorry, let me add one point, it could be the conflict comes from r* and r0. r0 is the rmin (the energetically most favorable distance of
two atoms), but r* is the sigma?
I need really your help.
thanks
Eliac

--- On Sat, 11/20/10, Eliac Brown <eliacbrown.yahoo.com> wrote:

> From: Eliac Brown <eliacbrown.yahoo.com>
> Subject: Re: [AMBER] non-bonding parameters
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Saturday, November 20, 2010, 12:09 AM
> 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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> > > >
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> > > --
> > > 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 - 16:30:04 PST
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