AMBER Archive (2008)

Subject: Re: AMBER: gaff paramters

From: Servaas Michielssens (servaas.michielssens_at_student.kuleuven.be)
Date: Fri Feb 22 2008 - 15:15:23 CST

I just noticed that I did not download the latest gaff.dat file. There
are other more realistic parameters in there.

Sorry for my to fast post.

greetz,

servaas

Quoting servaas michielssens <servaas.michielssens_at_student.kuleuven.be>:

> Dear,
>
> I was making a new topology for a molecule that contains a P-N
> bound, I used the gaff.dat file to generate the new paramters. When
> I had a look at the new paramters the gaff parameters for the
> X-p5-n3-X in the gaff suprized me:
> X -n3-p5-X 6 18.000 180.000 2.000
>
> I expected:
> 1. the forceconstant value to be much lower
> 2. the phase to be 0
> 3. pn to be 3
>
> So I decided to recalculated the parameter for the molecule in the
> attachement, I followed the strategie as in J.comput chem 24:
> 1016-1025, 2003.
> Results point out that the function is nothing like the parameters
> in the gaff but a much more complicated function. It cannot be fit
> with 1 cosine function (which is no problem of course) and barriere
> is +/- 2kcal/mol (Vmax).
>
> Their was also another problem:
> gaff:
> o -p5-o 46.0 115.80 SOURCE3 17 4.6921 5.7902
> parm99.dat:
> O2-P -O2 140.0 119.90
> Their must be something wrong with the force constant in the amber
> gaff.dat here (or my interpretation of them)...
> same for:
> o -p5-oh 43.8 115.03 SOURCE3 86 3.5330 4.9414
>
>
> Sincerely,
>
> servaas michielssens

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