AMBER Archive (2007)

Subject: Re: AMBER: frcmod file and NONB for dummy atoms

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Nov 23 2007 - 20:26:37 CST

Dear Dave,

I checked out amber.c to see what leap was doing while loading an frcmod
file. When it loads an frcmod file, it checks out each line and if it sees
NONB, it reads the NONB paramaters. This means that whether RE/SK/AC is
defined next to NONB is not important. When it reads the NONB parameters,
it uses the following line:

iRead = sscanf( sLine, "%s %lf %lf", saStr[0], &dRStar, &dDepth );

I guess here dRStar is the van der Waals radius and dDepth is the
potential depth of the NONB interaction.

I think it will be useful and will make things clear to change the file
format information on NONB part of frcmod in

http://amber.scripps.edu/formats.html#frcmod

to say that NONB parameters given in frcmod files should be the van der
Waals radius and the potential depth. Thanks.

Best regards,

On Fri, 23 Nov 2007, David A. Case wrote:

> On Thu, Nov 22, 2007, Ilyas Yildirim wrote:
> >
> > The format of the frcmod file in
> >
> > http://amber.scripps.edu/formats.html#frcmod
> >
> > says that to define NONB terms for the new atom types, follow 10A, B or C.
> > For dummy atoms, we want this NONB term to be zero. In my frcmod file, I
> > have the following lines to define this NONB terms for the dummy atoms:
> >
> > -------------------------------
> > NONB
> > DH 1.0000 0.000
> > -------------------------------
> >
> > I have tested this way of definition and it gives zero vdw energy for the
> > dummy atoms.
> >
> > My question is the following: According to the format described in the
> > above website, someone has to define NONB in the following ways:
> >
> > NONB SK
> > (Slater-Kirkwood parameters are input)
> >
> > or
> >
> > NONB RE
> > (van der Waals radius and the potential well depth)
> >
> > or
> >
> > NONB AC
> > (The 6-12 potential coefficients)
> >
> > My question is, what is the right way to define this NONB terms? In DAC's
> > TI tutorial, he also defines these NONB parameters without using SK/RE/AC.
> > Thanks in advance.
>
> I'm pretty sure frcmod only uses the "RE" form, and you don't have to specify
> it. If in doubt, you can look at the code to make sure.
>
> ...dac
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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