One last thing to take into account: non-bonded interactions are not
calculated for atoms within 1 or 2 bonds of each other (that form a bond or
an angle, that is). Furthermore, those that are 3 bonds away (forming a
dihedral), are, by default, scaled by 1.2 for electrostatics and 2.0 for
VDW, I believe (what used to be scee and scnb in amber10 and older before
variable 1-4 scaling was implemented in amber11).
Hope this helps,
Jason
On Mon, Aug 16, 2010 at 11:37 AM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Aug 16, 2010, Hector Chang wrote:
> >
> > I have a question about AMBER force field equation. I'm trying to
> > calculate the Van der Waals and Electrostatic part of the equation
> > and compare it with AMBER calculated value in the .out file. I used
> > A and B values from the "parm99.dat" and charge "q" from the amino
> > library files. I'm just running a 3 atoms system (CA, C, O - no bonds)
> > to check my calculation with AMBER. But my calculation and AMBER
> > calculated values for Van der Waals & Electrostatic do not match. I
> > wonder why. Please, any suggestions.
>
> It's great that you are trying to understand things in detail. The
> Amber page on file formats (http://ambermd.org/formats.html#parm.dat)
> and on units (http://ambermd.org/Questions/units.html) may help.
>
> First, the values in the parm.dat file are not "A" and "B", but r_min and
> eps,
> see http://ambermd.org/Questions/vdwequation.pdf.
>
> Second, you don't say how you are computing the electrostatics, but note
> that
> if compute q1*q2/r, with q in units of the electron charge and r in
> Angstroms,
> you need to multiple by about 332 to convert to kcal/mol.
>
> ...hope this helps....dac
>
>
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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 Mon Aug 16 2010 - 12:00:03 PDT
