Hi Hector,
First, check to be sure that you are calculating the van der Waals A
and B coefficients properly: http://ambermd.org/Questions/vdwequation.pdf
Second, check that you are multiplying the electrostatic energy by 332
(this converts from what I'll call quasi-cgs units to kcal/mol): http://ambermd.org/Questions/units.html
Best,
Paul
On Aug 16, 2010, at 8:26 AM, Hector Chang wrote:
> Hi,
>
> 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.
>
> Thanks,
> Hector
>
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Received on Mon Aug 16 2010 - 09:00:04 PDT
