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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Received on Mon Aug 16 2010 - 09:00:05 PDT
